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25 files changed, 753 insertions, 1242 deletions
diff --git a/README.org b/README.org index 94e9525..0b6f8bc 100644 --- a/README.org +++ b/README.org @@ -1,11 +1,78 @@ * guix-bioinformatics IMPORTANT: this repository lives at https://git.genenetwork.org/guix-bioinformatics/! -Older packages have been moved to https://git.genenetwork.org/guix-bioinformatics-past/. -Over 400 bioinformatics packages for Guix that are used in https://genenetwork.org/ and some other places. +Over 300 older packages have been moved to https://git.genenetwork.org/guix-bioinformatics-past/. Check out the README to see what packages are there. + +Over 300 bioinformatics packages for Guix that are used in https://genenetwork.org/ and some other places. Mostly targetting genomics, pangenomics and genetics. +** Pangenome tools (pangenomes meta-package) + +The =pangenomes= meta-package provides a comprehensive pangenomics toolkit: + +| Tool | Version | Description | +|----------------+--------------+------------------------------------------------| +| pggb | 0.7.4 | PanGenome Graph Builder pipeline | +| wfmash | 0.14.0 | Whole-genome Fuzzy Mapping and Alignment | +| seqwish | 0.7.11 | Sequence graph induction from alignments | +| smoothxg | 0.8.2 | Graph normalization via partial order alignment | +| odgi | 0.9.0 | Optimized Dynamic Genome/Graph Implementation | +| vg | 1.72.0 | Variation graph toolkit | +| impg | 0.4.1 | Implicit pangenome graph queries | +| minimap2 | 2.28 | Fast pairwise aligner (from Guix upstream) | +| bwa-mem2 | 2.3 | Burrows-Wheeler Aligner for short reads | +| samtools | 1.19 | SAM/BAM/CRAM manipulation (from Guix upstream) | +| htslib | 1.21 | HTSlib C library (from Guix upstream) | +| bedtools | 2.31.1 | Genome interval tools (from Guix upstream) | +| bcftools | 1.21 | VCF/BCF manipulation (from Guix upstream) | +| vcflib | 1.0.15 | VCF manipulation library and tools | +| vcfbub | 0.1.0 | VCF bubble popping | +| bandage-ng | 2026.4.1 | Assembly graph visualizer (Qt6) | +| gfalook | 0.1.0 | GFA visualization (odgi viz reimplementation) | +| pafplot | 0.1.0 | PAF alignment dotplot renderer | +| wally | 0.7.1 | Structural variant visualization | +| agc | 2.1 | Assembled Genomes Compressor | +| cigzip | 0.1.0 | CIGAR compression with tracepoints | +| cosigt | 0.1.7 | Pangenome haplotype genotyping | +| gfainject | 0.1.0 | BAM-to-GAF graph injection | +| gafpack | 0.0.0 | GAF coverage vector extraction | +| gfaffix | 0.2.1 | Walk-preserving graph simplification | +| gfautil | 0.4.0 | GFA format utilities | +| fastga-rs | 0.1.2 | Fast genome aligner (Rust) | +| fastix | 0.1.0 | FASTA header prefix renaming (PanSN) | +| kfilt | 0.1.1 | K-mer filtering | +| meryl | 1.4.1 | K-mer counting and set operations | +| miniprot | 0.18 | Protein-to-genome aligner | +| pangene | 1.1 | Gene-level pangenome analysis | +| rtg-tools | 3.13 | VCF evaluation (vcfeval) | + +** MEMPANG workshop (mempang-workshop meta-package) + +Extends =pangenomes= with R plotting, Python, and general utilities +for the MEMPANG pangenome workshop tutorials: + +| Category | Packages | +|----------------+------------------------------------------------------| +| R packages | r-ggplot2, r-tidyverse, r-ape, r-ggtree, r-gggenes | +| Python | python, python-igraph, python-pycairo | +| Utilities | graphviz, gnuplot, parallel, pigz, wget, zstd, bc | +| QC | multiqc, mummer | + +** GeneNetwork packages + +| Package | Version | Description | +|----------------------+--------------+---------------------------------------| +| genenetwork2 | 3.11 | GeneNetwork2 web application | +| genenetwork3 | 0.1.0 | GeneNetwork3 REST API | +| gn-auth | 1.0.1 | GN authentication service | +| gn-guile | 4.0.0 | Guile utilities for GN | +| gn-libs | 0.0.0 | Shared Python libraries | +| gn-uploader | 0.1.1 | Data uploader | +| gemma-wrapper | 0.99.6 | GEMMA CLI wrapper | +| gemma-gn2 | 0.98.5 | GEMMA for GeneNetwork2 | +| genecup | 1.8 | GeneCup literature mining | + See Guix documentation and [[https://gitlab.com/pjotrp/guix-notes/blob/master/HACKING.org][Guix notes]] for installing and hacking Guix. See [[https://github.com/franzos/awesome-guix][awesome guix]] for a list of other channels. @@ -23,7 +90,7 @@ To easily use the packages from this repo, simply add it to your `channels` list and run /guix pull/ like normal to update your software. E.g. #+BEGIN_SRC sh - guix pull --url=https://codeberg.org/guix/guix -p ~/opt/guix-pull --channels=channels.scm + guix pull --url=https://codeberg.org/guix/guix -p ~/opt/guix-bioinformatics --channels=channels.scm #+END_SRC The channel file actually accesses https://git.genenetwork.org/guix-bioinformatics/tree/.guix-channel which pulls other channels and fixates the hashes. The commit hash b0fa1dc can be found from the guix you want to run with /guix -V/, it speeds up installation and makes it reproducible. Note that the upstream channel may override that version. diff --git a/gn/packages/patches/do-not-build-cplusplus-spoa.patch b/do-not-build-cplusplus-spoa.patch index b9afb9a..b9afb9a 100644 --- a/gn/packages/patches/do-not-build-cplusplus-spoa.patch +++ b/do-not-build-cplusplus-spoa.patch diff --git a/gn/packages/mail.scm b/gn/packages/mail.scm new file mode 100644 index 0000000..dc2f2a3 --- /dev/null +++ b/gn/packages/mail.scm @@ -0,0 +1,20 @@ +(define-module (gn packages mail) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix gexp) + #:use-module (guix packages) + #:use-module (guix utils) + #:use-module (gnu packages) + #:use-module (gnu packages mail)) + +(define-public opensmtpd-patched + (package + (inherit opensmtpd) + (name "opensmtpd-patched") + (source + (origin + (inherit (package-source opensmtpd)) + (patches (search-patches "opensmtpd-gn-fixes.patch")))) + (synopsis "Lightweight SMTP daemon (with GN patches)") + (description + "OpenSMTPD with patches for missing grp.h include, TLS option +parsing fix, and timezone fallback for systems without tm_gmtoff."))) diff --git a/gn/packages/pangenome-rust.scm b/gn/packages/pangenome-rust.scm index fffd077..a488375 100644 --- a/gn/packages/pangenome-rust.scm +++ b/gn/packages/pangenome-rust.scm @@ -1548,7 +1548,7 @@ (file-name (git-file-name "rust-spoa-rs" "0.1.0.6f4f102")) (sha256 (base32 "13hmxqk70c0728v8l44qap25qla4w86im3kwfmay7jwwg9lk7lfg")) (patches - (list (local-file "patches/do-not-build-cplusplus-spoa.patch"))))) + (search-patches "do-not-build-cplusplus-spoa.patch")))) (define rust-stable-deref-trait-1.2.1 (crate-source "stable_deref_trait" "1.2.1" @@ -2333,6 +2333,190 @@ (crate-source "vcf" "0.6.1" "0dc0p00a19rpmhrqcshrn2qg5l716b5s1fy8vpd3p32bw77vpbs0")) +;; cigzip-specific crates +(define rust-cc-1.2.60 + (crate-source "cc" "1.2.60" + "084a8ziprdlyrj865f3303qr0b7aaggilkl18slncss6m4yp1ia3")) + + +(define rust-icu-collections-2.2.0 + (crate-source "icu_collections" "2.2.0" + "070r7xd0pynm0hnc1v2jzlbxka6wf50f81wybf9xg0y82v6x3119")) + + +(define rust-icu-locale-core-2.2.0 + (crate-source "icu_locale_core" "2.2.0" + "0a9cmin5w1x3bg941dlmgszn33qgq428k7qiqn5did72ndi9n8cj")) + + +(define rust-icu-normalizer-2.2.0 + (crate-source "icu_normalizer" "2.2.0" + "1d7krxr0xpc4x9635k1100a24nh0nrc59n65j6yk6gbfkplmwvn5")) + +(define rust-icu-normalizer-data-2.2.0 + (crate-source "icu_normalizer_data" "2.2.0" + "0f5d5d5fhhr9937m2z6z38fzh6agf14z24kwlr6lyczafypf0fys")) + + + +(define rust-icu-properties-2.2.0 + (crate-source "icu_properties" "2.2.0" + "1pkh3s837808cbwxvfagwc28cvwrz2d9h5rl02jwrhm51ryvdqxy")) + +(define rust-icu-properties-data-2.2.0 + (crate-source "icu_properties_data" "2.2.0" + "052awny0qwkbcbpd5jg2cd7vl5ry26pq4hz1nfsgf10c3qhbnawf")) + + + +(define rust-icu-provider-2.2.0 + (crate-source "icu_provider" "2.2.0" + "08dl8pxbwr8zsz4c5vphqb7xw0hykkznwi4rw7bk6pwb3krlr70k")) + + +(define rust-js-sys-0.3.95 + ;; TODO REVIEW: Check bundled sources. + (crate-source "js-sys" "0.3.95" + "1jhj3kgxxgwm0cpdjiz7i2qapqr7ya9qswadmr63dhwx3lnyjr19")) + + +(define rust-lib-wfa2-0.1.0.8859b6a + ;; TODO REVIEW: Define standalone package if this is a workspace. + (origin + (method git-fetch) + (uri (git-reference (url "https://github.com/AndreaGuarracino/lib_wfa2") + (commit "8859b6a214141968f37d9bcb22552408318adda0"))) + (file-name (git-file-name "rust-lib-wfa2" "0.1.0.8859b6a")) + (sha256 (base32 "08hfx5pzcmvk7pnxhjg6nvf77ng9rjrnysynj0qf6n6xd4n02qxa")))) + + +(define rust-libz-sys-1.1.28 + ;; TODO REVIEW: Check bundled sources. + (crate-source "libz-sys" "1.1.28" + "08hyf9v85zifl3353xc7i5wr53v9b3scri856cmphl3gaxp24fpw")) + + +(define rust-litemap-0.8.2 + (crate-source "litemap" "0.8.2" + "1w7628bc7wwcxc4n4s5kw0610xk06710nh2hn5kwwk2wa91z9nlj")) + + +(define rust-pkg-config-0.3.33 + (crate-source "pkg-config" "0.3.33" + "17jnqmcbxsnwhg9gjf0nh6dj5k0x3hgwi3mb9krjnmfa9v435w8r")) + + +(define rust-portable-atomic-util-0.2.7 + (crate-source "portable-atomic-util" "0.2.7" + "0616j0fhy6y71hyxg3n86f6hng0fmsc269s3wp4gl8ww4p8hd8f2")) + + +(define rust-potential-utf-0.1.5 + (crate-source "potential_utf" "0.1.5" + "0r0518fr32xbkgzqap509s3r60cr0iancsg9j1jgf37cyz7b20q1")) + + +(define rust-ragc-common-0.1.1.40e5cad + ;; TODO REVIEW: Define standalone package if this is a workspace. + (origin + (method git-fetch) + (uri (git-reference (url "https://github.com/ekg/ragc") + (commit "40e5cad11cab7d4df07a72d6b16d68c2d60b0742"))) + (file-name (git-file-name "rust-ragc-common" "0.1.1.40e5cad")) + (sha256 (base32 "1p71jj02ppcvkrvnbs4y0yf00cslzqhlx4idscx8fk4lhmip4kla")))) + + +(define rust-ragc-core-0.1.1.40e5cad + ;; TODO REVIEW: Define standalone package if this is a workspace. + (origin + (method git-fetch) + (uri (git-reference (url "https://github.com/ekg/ragc") + (commit "40e5cad11cab7d4df07a72d6b16d68c2d60b0742"))) + (file-name (git-file-name "rust-ragc-core" "0.1.1.40e5cad")) + (sha256 (base32 "1p71jj02ppcvkrvnbs4y0yf00cslzqhlx4idscx8fk4lhmip4kla")))) + + +(define rust-tinystr-0.8.3 + (crate-source "tinystr" "0.8.3" + "0vfr8x285w6zsqhna0a9jyhylwiafb2kc8pj2qaqaahw48236cn8")) + + +(define rust-wasm-bindgen-0.2.118 + (crate-source "wasm-bindgen" "0.2.118" + "129s5r14fx4v4xrzpx2c6l860nkxpl48j50y7kl6j16bpah3iy8b")) + +(define rust-wasm-bindgen-macro-0.2.118 + (crate-source "wasm-bindgen-macro" "0.2.118" + "1v98r8vs17cj8918qsg0xx4nlg4nxk1g0jd4nwnyrh1687w29zzf")) + +(define rust-wasm-bindgen-macro-support-0.2.118 + (crate-source "wasm-bindgen-macro-support" "0.2.118" + "0169jr0q469hfx5zqxfyywf2h2f4aj17vn4zly02nfwqmxghc24x")) + +(define rust-wasm-bindgen-shared-0.2.118 + (crate-source "wasm-bindgen-shared" "0.2.118" + "0ag1vvdzi4334jlzilsy14y3nyzwddf1ndn62fyhf6bg62g4vl2z")) + + + + + +(define rust-web-sys-0.3.95 + ;; TODO REVIEW: Check bundled sources. + (crate-source "web-sys" "0.3.95" + "0zfr2jy5bpkkggl88i43yy37p538hg20i56kwn421yj9g6qznbag")) + + +(define rust-writeable-0.6.3 + (crate-source "writeable" "0.6.3" + "1i54d13h9bpap2hf13xcry1s4lxh7ap3923g8f3c0grd7c9fbyhz")) + + +(define rust-yoke-0.8.2 + (crate-source "yoke" "0.8.2" + "1jprcs7a98a5whvfs6r3jvfh1nnfp6zyijl7y4ywmn88lzywbs5b")) + +(define rust-yoke-derive-0.8.2 + (crate-source "yoke-derive" "0.8.2" + "13l5y5sz4lqm7rmyakjbh6vwgikxiql51xfff9hq2j485hk4r16y")) + + + +(define rust-zerocopy-0.8.48 + (crate-source "zerocopy" "0.8.48" + "1sb8plax8jbrsng1jdval7bdhk7hhrx40dz3hwh074k6knzkgm7f")) + +(define rust-zerocopy-derive-0.8.48 + (crate-source "zerocopy-derive" "0.8.48" + "1m5s0g92cxggqc74j83k1priz24k3z93sj5gadppd20p9c4cvqvh")) + + + +(define rust-zerofrom-0.1.7 + (crate-source "zerofrom" "0.1.7" + "1py40in4rirc9q8w36q67pld0zk8ssg024xhh0cncxgal7ra3yk9")) + +(define rust-zerofrom-derive-0.1.7 + (crate-source "zerofrom-derive" "0.1.7" + "18c4wsnznhdxx6m80piil1lbyszdiwsshgjrybqcm4b6qic22lqi")) + + + +(define rust-zerotrie-0.2.4 + (crate-source "zerotrie" "0.2.4" + "1gr0pkcn3qsr6in6iixqyp0vbzwf2j1jzyvh7yl2yydh3p9m548g")) + + +(define rust-zerovec-0.11.6 + (crate-source "zerovec" "0.11.6" + "0fdjsy6b31q9i0d73sl7xjd12xadbwi45lkpfgqnmasrqg5i3ych")) + +(define rust-zerovec-derive-0.11.3 + (crate-source "zerovec-derive" "0.11.3" + "0m85qj92mmfvhjra6ziqky5b1p4kcmp5069k7kfadp5hr8jw8pb2")) + + + ;; pafplot-specific crates (define rust-boomphf-0.6.0 (crate-source "boomphf" "0.6.0" @@ -3511,7 +3695,215 @@ rust-utf8parse-0.2.2 rust-version-check-0.9.5 rust-windows-link-0.2.1 - rust-windows-sys-0.61.2))) + rust-windows-sys-0.61.2)) + (cigzip => + (list rust-adler2-2.0.1 + rust-ahash-0.8.12 + rust-aho-corasick-1.1.4 + rust-allocator-api2-0.2.21 + rust-anes-0.1.6 + rust-anstream-1.0.0 + rust-anstyle-1.0.14 + rust-anstyle-parse-1.0.0 + rust-anstyle-query-1.1.5 + rust-anstyle-wincon-3.0.11 + rust-anyhow-1.0.102 + rust-arbitrary-chunks-0.4.1 + rust-autocfg-1.5.0 + rust-bgzip-0.3.1 + rust-bincode-1.3.3 + rust-bindgen-0.69.5 + rust-bio-types-1.0.4 + rust-bitflags-2.11.1 + rust-block-buffer-0.10.4 + rust-block-pseudorand-0.1.2 + rust-bumpalo-3.20.2 + rust-byteorder-1.5.0 + rust-bytes-1.11.1 + rust-cast-0.3.0 + rust-cc-1.2.60 + rust-cexpr-0.6.0 + rust-cfg-if-1.0.4 + rust-chiapos-chacha8-0.1.0 + rust-ciborium-0.2.2 + rust-ciborium-io-0.2.2 + rust-ciborium-ll-0.2.2 + rust-clang-sys-1.8.1 + rust-clap-4.6.1 + rust-clap-builder-4.6.0 + rust-clap-derive-4.6.1 + rust-clap-lex-1.1.0 + rust-cmake-0.1.58 + rust-colorchoice-1.0.5 + rust-console-0.16.3 + rust-cpufeatures-0.2.17 + rust-crc32fast-1.5.0 + rust-criterion-0.5.1 + rust-criterion-plot-0.5.0 + rust-crossbeam-0.8.4 + rust-crossbeam-channel-0.5.15 + rust-crossbeam-deque-0.8.6 + rust-crossbeam-epoch-0.9.18 + rust-crossbeam-queue-0.3.12 + rust-crossbeam-utils-0.8.21 + rust-crunchy-0.2.4 + rust-crypto-common-0.1.7 + rust-custom-derive-0.1.7 + rust-dashmap-6.1.0 + rust-derive-new-0.6.0 + rust-derive-new-0.7.0 + rust-digest-0.10.7 + rust-displaydoc-0.2.5 + rust-either-1.15.0 + rust-encode-unicode-1.0.0 + rust-env-filter-1.0.1 + rust-env-logger-0.11.10 + rust-find-msvc-tools-0.1.9 + rust-flate2-1.1.9 + rust-form-urlencoded-1.2.2 + rust-fs-utils-1.1.4 + rust-generic-array-0.14.7 + rust-getrandom-0.3.4 + rust-glob-0.3.3 + rust-half-2.7.1 + rust-hashbrown-0.14.5 + rust-heck-0.5.0 + rust-hermit-abi-0.5.2 + rust-hts-sys-2.2.0 + rust-icu-collections-2.2.0 + rust-icu-locale-core-2.2.0 + rust-icu-normalizer-2.2.0 + rust-icu-normalizer-data-2.2.0 + rust-icu-properties-2.2.0 + rust-icu-properties-data-2.2.0 + rust-icu-provider-2.2.0 + rust-idna-1.1.0 + rust-idna-adapter-1.2.1 + rust-ieee754-0.2.6 + rust-indicatif-0.18.4 + rust-is-terminal-0.4.17 + rust-is-terminal-polyfill-1.70.2 + rust-itertools-0.10.5 + rust-itertools-0.12.1 + rust-itoa-1.0.18 + rust-jiff-0.2.23 + rust-jiff-static-0.2.23 + rust-jobserver-0.1.34 + rust-js-sys-0.3.95 + rust-lazy-static-1.5.0 + rust-lazycell-1.3.0 + rust-lib-wfa2-0.1.0.8859b6a + rust-libc-0.2.185 + rust-libdeflate-sys-1.25.2 + rust-libloading-0.8.9 + rust-libz-sys-1.1.28 + rust-linear-map-1.2.0 + rust-litemap-0.8.2 + rust-lock-api-0.4.14 + rust-log-0.4.29 + rust-memchr-2.8.0 + rust-minimal-lexical-0.2.1 + rust-miniz-oxide-0.8.9 + rust-nanorand-0.6.1 + rust-newtype-derive-0.1.6 + rust-nom-7.1.3 + rust-noodles-0.100.0 + rust-noodles-bgzf-0.42.0 + rust-num-traits-0.2.19 + rust-num-cpus-1.17.0 + rust-once-cell-1.21.4 + rust-once-cell-polyfill-1.70.2 + rust-oorandom-11.1.5 + rust-parking-lot-core-0.9.12 + rust-partition-0.1.2 + rust-percent-encoding-2.3.2 + rust-pkg-config-0.3.33 + rust-plotters-0.3.7 + rust-plotters-backend-0.3.7 + rust-plotters-svg-0.3.7 + rust-portable-atomic-1.13.1 + rust-portable-atomic-util-0.2.7 + rust-potential-utf-0.1.5 + rust-proc-macro2-1.0.106 + rust-quick-error-1.2.3 + rust-quote-1.0.45 + rust-r-efi-5.3.0 + rust-ragc-common-0.1.1.40e5cad + rust-ragc-core-0.1.1.40e5cad + rust-rayon-1.12.0 + rust-rayon-core-1.13.0 + rust-rdst-0.20.14 + rust-redox-syscall-0.5.18 + rust-regex-1.12.3 + rust-regex-automata-0.4.14 + rust-regex-syntax-0.8.10 + rust-rust-htslib-1.0.0 + rust-rustc-hash-1.1.0 + rust-rustc-version-0.1.7 + rust-rustversion-1.0.22 + rust-same-file-1.0.6 + rust-scopeguard-1.2.0 + rust-semver-0.1.20 + rust-serde-1.0.228 + rust-serde-core-1.0.228 + rust-serde-derive-1.0.228 + rust-serde-json-1.0.149 + rust-sha2-0.10.9 + rust-shlex-1.3.0 + rust-simd-adler32-0.3.9 + rust-smallvec-1.15.1 + rust-stable-deref-trait-1.2.1 + rust-strsim-0.11.1 + rust-strum-macros-0.26.4 + rust-syn-2.0.117 + rust-synstructure-0.13.2 + rust-thiserror-1.0.69 + rust-thiserror-2.0.18 + rust-thiserror-impl-1.0.69 + rust-thiserror-impl-2.0.18 + rust-tikv-jemalloc-sys-0.5.4+5.3.0-patched + rust-tikv-jemallocator-0.5.4 + rust-tinystr-0.8.3 + rust-tinytemplate-1.2.1 + rust-tpa-0.1.0.49f1801 + rust-tracepoints-0.1.0.66a5511 + rust-typenum-1.19.0 + rust-unicode-ident-1.0.24 + rust-unicode-width-0.2.2 + rust-unit-prefix-0.5.2 + rust-url-2.5.8 + rust-utf8-iter-1.0.4 + rust-utf8parse-0.2.2 + rust-vcpkg-0.2.15 + rust-version-check-0.9.5 + rust-voracious-radix-sort-1.2.0 + rust-walkdir-2.5.0 + rust-wasip2-1.0.2+wasi-0.2.9 + rust-wasm-bindgen-0.2.118 + rust-wasm-bindgen-macro-0.2.118 + rust-wasm-bindgen-macro-support-0.2.118 + rust-wasm-bindgen-shared-0.2.118 + rust-web-sys-0.3.95 + rust-web-time-1.1.0 + rust-winapi-util-0.1.11 + rust-windows-link-0.2.1 + rust-windows-sys-0.61.2 + rust-wit-bindgen-0.51.0 + rust-writeable-0.6.3 + rust-yoke-0.8.2 + rust-yoke-derive-0.8.2 + rust-zerocopy-0.8.48 + rust-zerocopy-derive-0.8.48 + rust-zerofrom-0.1.7 + rust-zerofrom-derive-0.1.7 + rust-zerotrie-0.2.4 + rust-zerovec-0.11.6 + rust-zerovec-derive-0.11.3 + rust-zlib-rs-0.6.3 + rust-zmij-1.0.21 + rust-zstd-0.13.3 + rust-zstd-safe-7.2.4 + rust-zstd-sys-2.0.16+zstd.1.5.7))) ;;; ;;; Main package. @@ -3526,7 +3918,7 @@ (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/pangenome/gfainject") + (url "https://github.com/chfi/gfainject") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -3539,7 +3931,7 @@ ;; No upstream test data; tests require GFA/BAM input files. (inputs (cargo-inputs 'gfainject #:module '(gn packages pangenome-rust))) (properties '((tunable? . #t))) - (home-page "https://github.com/pangenome/gfainject") + (home-page "https://github.com/chfi/gfainject") (synopsis "Map BAM alignments to GFA graph paths as GAF records") (description "Gfainject maps read alignments from a BAM file to reference paths in a diff --git a/gn/packages/pangenome.scm b/gn/packages/pangenome.scm index b83455b..dae4487 100644 --- a/gn/packages/pangenome.scm +++ b/gn/packages/pangenome.scm @@ -14,6 +14,8 @@ #:use-module (guix build-system gnu) #:use-module (guix build-system go) #:use-module (guix build-system trivial) + #:use-module (gnu packages) + #:use-module (gnu packages assembly) #:use-module (gnu packages base) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages boost) @@ -38,13 +40,16 @@ #:use-module (gnu packages time) #:use-module (gnu packages bash) #:use-module (gnu packages check) + #:use-module (gnu packages c) #:use-module (gnu packages cpp) #:use-module (gnu packages curl) #:use-module (gnu packages documentation) #:use-module (gnu packages elf) + #:use-module (gnu packages graphviz) #:use-module (gnu packages gtk) #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages java) + #:use-module (gnu packages llvm) #:use-module (gnu packages ncurses) #:use-module (gnu packages protobuf) #:use-module (gnu packages qt) @@ -82,12 +87,17 @@ "1b5s2b19hybr2r0mxch5x5f0gzy77w1xcfp2js4rprqr8dimppak")))) (build-system gnu-build-system) (arguments - (list #:tests? #f + (list #:tests? #f ; no test target in CMake build #:make-flags #~(list (string-append "CC=" #$(cc-for-target))) #:phases #~(modify-phases %standard-phases (delete 'configure) + (add-after 'unpack 'fix-missing-includes + (lambda _ + (substitute* (find-files "src" "\\.(h|cpp)$") + (("#include <vector>" all) + (string-append "#include <cstdint>\n" all))))) ;; -DSTDC_HEADERS tells safeclib_private.h to include ;; stdlib.h/ctype.h unconditionally (normally set by autoconf). (add-before 'build 'fix-cflags @@ -136,7 +146,7 @@ perform bounds checking and return meaningful error codes.") "01dhryf6nbdicrvbdk4mrdypm0l9vqh1qis9qp0pdh8qbxgh060c")))) (build-system gnu-build-system) (arguments - (list #:tests? #f + (list #:tests? #f ; no test target in Makefile #:make-flags #~(list (string-append "CC=" #$(cc-for-target)) (string-append "CXX=" #$(cxx-for-target))) @@ -167,6 +177,11 @@ perform bounds checking and return meaningful error codes.") (("\tcd ext/safestringlib/ && \\$\\(MAKE\\) clean\n") ""))))) (delete 'configure) + (add-after 'unpack 'fix-missing-includes + (lambda _ + (substitute* (find-files "src" "\\.(h|cpp)$") + (("#include <vector>" all) + (string-append "#include <cstdint>\n" all))))) (replace 'install (lambda _ (mkdir-p (string-append #$output "/bin")) @@ -210,6 +225,11 @@ with a runtime dispatcher.") #:phases #~(modify-phases %standard-phases (delete 'configure) + (add-after 'unpack 'fix-missing-includes + (lambda _ + (substitute* (find-files "src" "\\.(h|cpp)$") + (("#include <vector>" all) + (string-append "#include <cstdint>\n" all))))) (replace 'check (lambda _ (invoke "./miniprot" @@ -253,6 +273,11 @@ protein-coding genes in a new genome using related genomes as references.") #:phases #~(modify-phases %standard-phases (delete 'configure) + (add-after 'unpack 'fix-missing-includes + (lambda _ + (substitute* (find-files "src" "\\.(h|cpp)$") + (("#include <vector>" all) + (string-append "#include <cstdint>\n" all))))) (replace 'check (lambda _ (invoke "./pangene" "test/C4/21GRCh38-renamed.paf.gz" @@ -292,7 +317,7 @@ suitable for downstream pangenome analysis.") (native-inputs (list pkg-config)) (inputs (list boost htslib opencv zlib xz bzip2)) (arguments - (list #:tests? #f + (list #:tests? #f ; no test target in Makefile #:make-flags #~(list (string-append "CXX=" #$(cxx-for-target)) ;; Point to installed htslib; Makefile uses EBROOTHTSLIB as @@ -305,6 +330,11 @@ suitable for downstream pangenome analysis.") #:phases #~(modify-phases %standard-phases (delete 'configure) + (add-after 'unpack 'fix-missing-includes + (lambda _ + (substitute* (find-files "src" "\\.(h|cpp)$") + (("#include <vector>" all) + (string-append "#include <cstdint>\n" all))))) (add-after 'unpack 'fix-makefile (lambda _ (substitute* "Makefile" @@ -352,13 +382,18 @@ and heatmaps for structural variant and genome assembly analysis.") (build-system gnu-build-system) (native-inputs (list perl which)) (arguments - (list #:tests? #f + (list #:tests? #f ; no test target in Makefile #:make-flags #~(list (string-append "CC=" #$(cc-for-target)) (string-append "CXX=" #$(cxx-for-target))) #:phases #~(modify-phases %standard-phases (delete 'configure) + (add-after 'unpack 'fix-missing-includes + (lambda _ + (substitute* (find-files "src" "\\.(h|cpp)$") + (("#include <vector>" all) + (string-append "#include <cstdint>\n" all))))) (add-before 'build 'chdir-src (lambda _ (chdir "src"))) (replace 'install @@ -492,7 +527,8 @@ pangene.") (build-system cmake-build-system) (arguments (list - #:tests? #f + #:tests? #f ; tests are bash scripts (test_binary.sh) and python doctests + ; that require test data and a python odgi module import #:parallel-build? #f ; OOM with parallel build #:phases #~(modify-phases %standard-phases @@ -540,8 +576,8 @@ graph model, as well as algorithms for pangenome analysis.") (sha256 (base32 "18wsrvqf0nsfk29v3ggdq2r4q15d4n4sq8v228qq1jsybbjlkgsa")) (patches - (list (local-file "patches/seqwish-paryfor-riscv.patch") - (local-file "patches/seqwish-shared-library.patch"))) + (search-patches "seqwish-paryfor-riscv.patch" + "seqwish-shared-library.patch")) (snippet #~(begin (use-modules (guix build utils)) @@ -789,7 +825,7 @@ sequences using wfmash, seqwish, smoothxg, and gfaffix.") (("-march=native ") "")))))) (arguments (substitute-keyword-arguments (package-arguments wfmash) - ((#:tests? tests? #f) #f) + ((#:tests? tests? #f) #f) ; inherit from wfmash; same rationale ((#:phases phases #~%standard-phases) #~(modify-phases #$phases (delete 'install-scripts) @@ -908,6 +944,11 @@ manipulations on VCF files.") #:phases #~(modify-phases %standard-phases (delete 'configure) ; no configure script + (add-after 'unpack 'fix-missing-includes + (lambda _ + (substitute* (find-files "src" "\\.(h|cpp)$") + (("#include <vector>" all) + (string-append "#include <cstdint>\n" all))))) (add-after 'unpack 'patch-source (lambda* (#:key inputs #:allow-other-keys) ;; Add subdirectory include paths for system packages @@ -1292,6 +1333,116 @@ sequence data including @code{vcfeval} for variant comparison, sequence data simulators, and format conversion utilities.") (license license:bsd-2))) +;; tracepoints is a library-only Rust crate (no CLI binary); its +;; functionality is exposed via the cigzip tool below. The crate source +;; is available as rust-tracepoints-0.1.0.66a5511 in pangenome-rust.scm +;; for use as a dependency. + +(define-public cigzip + (let ((commit "b7cc0ed6abb6515a8ad231d47ef90a06a3a491e8") + (revision "1")) + (package + (name "cigzip") + (version (git-version "0.1.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/AndreaGuarracino/cigzip") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0kmpwkxk86428z3iva2wx0x0aavqqnx0m2sblpvw5mdd4102xjhx")))) + (build-system cargo-build-system) + (arguments + (list #:install-source? #f + ;; Tests require WFA2 C library built in OUT_DIR via build.rs + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'copy-ragc-workspace + (lambda* (#:key inputs #:allow-other-keys) + ;; ragc has a workspace Cargo.toml; copy it locally and + ;; point dependents to the ragc-core subdir. + (let ((ragc (assoc-ref inputs + "rust-ragc-core-0.1.1.40e5cad-checkout"))) + (copy-recursively ragc "ragc-workspace")))) + (add-before 'build 'fix-dependency-sources + (lambda _ + ;; Rewrite all git deps of cigzip and its vendored + ;; transitive deps to use guix-vendor local paths. + (let ((cargo-tomls + (list "Cargo.toml" + "guix-vendor/rust-tpa-0.1.0.49f1801-checkout/Cargo.toml" + "guix-vendor/rust-tracepoints-0.1.0.66a5511-checkout/Cargo.toml"))) + (for-each + (lambda (file) + (when (file-exists? file) + (substitute* file + (("git = \"https://github.com/AndreaGuarracino/lib_wfa2\"[^,}]*(, rev = \"[0-9a-f]*\")?") + "path = \"../rust-lib-wfa2-0.1.0.8859b6a-checkout\", version = \"0.1.0\"") + (("git = \"https://github.com/AndreaGuarracino/tracepoints\"[^,}]*(, rev = \"[0-9a-f]*\")?") + "path = \"../rust-tracepoints-0.1.0.66a5511-checkout\", version = \"0.1.0\"") + (("git = \"https://github.com/AndreaGuarracino/tpa\"[^,}]*(, rev = \"[0-9a-f]*\")?") + "path = \"../rust-tpa-0.1.0.49f1801-checkout\", version = \"0.1.0\"") + (("git = \"https://github.com/ekg/ragc\", rev = \"40e5cad\"") + "path = \"ragc-workspace/ragc-core\", version = \"0.1.1\"")))) + cargo-tomls) + ;; The top-level Cargo.toml uses "ragc-workspace/ragc-core" + ;; (relative to package root), but vendored Cargo.tomls + ;; have sibling paths via ../ + (substitute* "Cargo.toml" + (("path = \"\\.\\./rust-lib-wfa2-0.1.0.8859b6a-checkout\"") + "path = \"guix-vendor/rust-lib-wfa2-0.1.0.8859b6a-checkout\"") + (("path = \"\\.\\./rust-tracepoints-0.1.0.66a5511-checkout\"") + "path = \"guix-vendor/rust-tracepoints-0.1.0.66a5511-checkout\"") + (("path = \"\\.\\./rust-tpa-0.1.0.49f1801-checkout\"") + "path = \"guix-vendor/rust-tpa-0.1.0.49f1801-checkout\""))))) + (add-before 'build 'patch-lib-wfa2-use-system + ;; Replace lib_wfa2 build.rs to link against system + ;; wfa2-lib-static instead of building from submodule. + (lambda _ + (let ((wfa2-build "guix-vendor/rust-lib-wfa2-0.1.0.8859b6a-checkout/build.rs")) + (chmod wfa2-build #o644) + (call-with-output-file wfa2-build + (lambda (port) + (display + (string-append + "fn main() {\n" + " println!(\"cargo:rustc-link-lib=static=wfa\");\n" + " println!(\"cargo:rustc-link-lib=gomp\");\n" + " println!(\"cargo:rustc-link-search=native=" + #$(file-append wfa2-lib-static "/lib") "\");\n" + "}\n") + port)))) + ;; Patch bindings_wfa.rs: cast_signed/cast_unsigned are + ;; unstable until Rust 1.87. + (substitute* + "guix-vendor/rust-lib-wfa2-0.1.0.8859b6a-checkout/src/bindings_wfa.rs" + (("u32::cast_signed\\(self\\._bitfield_1\\.get\\(0usize, 24u8\\) as u32\\)") + "((self._bitfield_1.get(0usize, 24u8) as u32) as i32)") + (("u32::cast_signed\\(<") + "((<") + ((" \\) as u32\\)") + " ) as u32) as i32)") + (("i32::cast_unsigned\\(val\\)") + "(val as u32)") + (("i32::cast_unsigned\\(_flags2\\)") + "(_flags2 as u32)"))))))) + (native-inputs (list pkg-config cmake-minimal clang)) + (inputs (cons* htslib + wfa2-lib-static + zlib + libdeflate + (list zstd "lib") + (cargo-inputs 'cigzip + #:module '(gn packages pangenome-rust)))) + (home-page "https://github.com/AndreaGuarracino/cigzip") + (synopsis "Compressed alignment representation using tracepoints") + (description "cigzip converts between CIGAR strings and tracepoint +representations for efficient alignment storage, using adaptive tracepoints +that segment based on local alignment complexity.") + (license license:expat)))) + (define-public gfalook (let ((commit "5199d77ecc4980b181177c16b94f6e56c0d06e4c") (revision "1")) @@ -1309,6 +1460,7 @@ simulators, and format conversion utilities.") (build-system cargo-build-system) (arguments (list #:install-source? #f + ;; No tests in crate (0 unit tests). #:tests? #f #:phases #~(modify-phases %standard-phases @@ -1343,8 +1495,7 @@ producing PNG and SVG visualizations of pangenome graphs in GFA format.") (base32 "0aisssmmss4jxgnv04qk5gbnzzbzvakkcdr03swps3f1x22rfqdn")))) (build-system cargo-build-system) (arguments - (list #:install-source? #f - #:tests? #f)) + (list #:install-source? #f)) (inputs (cargo-inputs 'pafplot #:module '(gn packages pangenome-rust))) (home-page "https://github.com/ekg/pafplot") @@ -1354,6 +1505,52 @@ raster dotplot images, drawing lines for each match to visualize homology between sequences.") (license license:expat)))) +(define-public agc + (package + (name "agc") + (version "2.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/refresh-bio/agc") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0qxrs52lnbm2296b15k1x7dgffv66chac16s7qalp8x0clyfnjgm")) + (snippet + #~(begin + (use-modules (guix build utils)) + (substitute* "makefile" + (("-mavx") "") + (("-m64") "")))))) + (build-system gnu-build-system) + (arguments + (list + #:tests? #f ; no test target + #:make-flags + #~(list (string-append "CC=" #$(cxx-for-target)) + "agc") + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (add-after 'unpack 'fix-missing-includes + (lambda _ + (substitute* (find-files "src" "\\.(h|cpp)$") + (("#include <vector>" all) + (string-append "#include <cstdint>\n" all))))) + (replace 'install + (lambda _ + (install-file "agc" (string-append #$output "/bin"))))))) + (home-page "https://github.com/refresh-bio/agc") + (synopsis "Assembled Genomes Compressor") + (description + "AGC is a tool designed to compress collections of de-novo assembled +genomes. It achieves high compression ratios using a reference-based approach +and can be used for various types of datasets from short viral genomes to +long human genomes.") + (license license:expat))) + (define-public pangenomes (package (name "pangenomes") @@ -1367,15 +1564,17 @@ between sequences.") (use-modules (guix build utils)) (mkdir-p (string-append #$output "/bin"))))) (propagated-inputs - (list bandage-ng + (list agc + bandage-ng bedtools bwa-mem2 + cigzip cosigt fastga-rs gafpack + gfalook gfaffix gfainject - gfalook gfautil htslib impg @@ -1394,7 +1593,7 @@ between sequences.") vcflib vg wally - wfmash)) + wfmash-0.14)) (home-page "https://github.com/pangenome") (synopsis "Pangenome tools collection") (description "Meta package that provides the main pangenome tools: @@ -1419,8 +1618,12 @@ kfilt, miniprot, pangene, wally, and vcfbub.") (list pangenomes bc bcftools + coreutils fastix gnuplot + graphviz + grep + gzip multiqc mummer pafplot @@ -1431,6 +1634,7 @@ kfilt, miniprot, pangene, wally, and vcfbub.") python-pycairo rtg-tools r-minimal + sed r-ape r-data-table r-gggenes diff --git a/gn/packages/patches/arrayfire-lapack-detection.patch b/gn/packages/patches/arrayfire-lapack-detection.patch deleted file mode 100644 index 1925122..0000000 --- a/gn/packages/patches/arrayfire-lapack-detection.patch +++ /dev/null @@ -1,277 +0,0 @@ -https://sources.debian.org/data/main/a/arrayfire/3.3.2+dfsg1-4/debian/patches/Fix-LAPACKE-detection.patch - -From: Ghislain Antony Vaillant <ghisvail@gmail.com> -Date: Wed, 2 Mar 2016 10:46:50 +0000 -Subject: Fix LAPACKE detection. - ---- - CMakeModules/FindLAPACKE.cmake | 54 +++++++++++++++------------------------ - src/backend/cpu/CMakeLists.txt | 18 ++++++------- - src/backend/cuda/CMakeLists.txt | 11 ++++---- - src/backend/opencl/CMakeLists.txt | 19 +++++++------- - 4 files changed, 45 insertions(+), 57 deletions(-) - -diff --git a/CMakeModules/FindLAPACKE.cmake b/CMakeModules/FindLAPACKE.cmake -index 9251ee9..1a73632 100644 ---- a/CMakeModules/FindLAPACKE.cmake -+++ b/CMakeModules/FindLAPACKE.cmake -@@ -4,13 +4,13 @@ - # FIND_PACKAGE(LAPACKE [REQUIRED] [QUIET] ) - # - # It sets the following variables: --# LAPACK_FOUND ... true if LAPACKE is found on the system --# LAPACK_LIBRARIES ... full path to LAPACKE library --# LAPACK_INCLUDES ... LAPACKE include directory --# -+# LAPACKE_FOUND ... true if LAPACKE is found on the system -+# LAPACKE_INCLUDE_DIRS ... LAPACKE include directories -+# LAPACKE_LIBRARIES ... path to LAPACKE libraries -+# LAPACKE_LIBRARY_DIRS ... LAPACKE library directories - - SET(LAPACKE_ROOT_DIR CACHE STRING -- "Root directory for custom LAPACK implementation") -+ "Root directory for custom LAPACKE implementation") - - IF (NOT INTEL_MKL_ROOT_DIR) - SET(INTEL_MKL_ROOT_DIR $ENV{INTEL_MKL_ROOT}) -@@ -40,29 +40,20 @@ IF(PKG_CONFIG_FOUND AND NOT LAPACKE_ROOT_DIR) - ENDIF() - - IF(PC_LAPACKE_FOUND) -+ -+ # Verify sanity of LAPACKE pkg-config file. - FOREACH(PC_LIB ${PC_LAPACKE_LIBRARIES}) - FIND_LIBRARY(${PC_LIB}_LIBRARY NAMES ${PC_LIB} HINTS ${PC_LAPACKE_LIBRARY_DIRS} ) - IF (NOT ${PC_LIB}_LIBRARY) - MESSAGE(FATAL_ERROR "Something is wrong in your pkg-config file - lib ${PC_LIB} not found in ${PC_LAPACKE_LIBRARY_DIRS}") - ENDIF (NOT ${PC_LIB}_LIBRARY) -- LIST(APPEND LAPACKE_LIB ${${PC_LIB}_LIBRARY}) - ENDFOREACH(PC_LIB) - -- FIND_PATH( -- LAPACKE_INCLUDES -- NAMES "lapacke.h" -- PATHS -- ${PC_LAPACKE_INCLUDE_DIRS} -- ${INCLUDE_INSTALL_DIR} -- /usr/include -- /usr/local/include -- /sw/include -- /opt/local/include -- DOC "LAPACKE Include Directory" -- ) -+ set(LAPACKE_LIBRARIES ${PC_LAPACKE_LIBRARIES}) -+ set(LAPACKE_LIBRARY_DIRS ${PC_LAPACKE_LIBRARY_DIRS}) - -- FIND_PACKAGE_HANDLE_STANDARD_ARGS(LAPACKE DEFAULT_MSG LAPACKE_LIB) -- MARK_AS_ADVANCED(LAPACKE_INCLUDES LAPACKE_LIB) -+ FIND_PATH(LAPACKE_INCLUDE_DIRS NAMES "lapacke.h" -+ PATHS ${PC_LAPACKE_INCLUDE_DIRS}) - - ELSE(PC_LAPACKE_FOUND) - -@@ -97,7 +88,6 @@ ELSE(PC_LAPACKE_FOUND) - LAPACKE_LIB - NAMES "lapacke" "liblapacke" "openblas" "mkl_rt" - PATHS -- ${PC_LAPACKE_LIBRARY_DIRS} - ${LIB_INSTALL_DIR} - /opt/intel/mkl/lib/ia32 - /opt/intel/mkl/lib/intel64 -@@ -113,7 +103,6 @@ ELSE(PC_LAPACKE_FOUND) - LAPACK_LIB - NAMES "lapack" "liblapack" "openblas" "mkl_rt" - PATHS -- ${PC_LAPACKE_LIBRARY_DIRS} - ${LIB_INSTALL_DIR} - /opt/intel/mkl/lib/ia32 - /opt/intel/mkl/lib/intel64 -@@ -129,7 +118,6 @@ ELSE(PC_LAPACKE_FOUND) - LAPACKE_INCLUDES - NAMES "lapacke.h" "mkl_lapacke.h" - PATHS -- ${PC_LAPACKE_INCLUDE_DIRS} - ${INCLUDE_INSTALL_DIR} - /opt/intel/mkl/include - /usr/include -@@ -141,17 +129,15 @@ ELSE(PC_LAPACKE_FOUND) - lapacke - ) - ENDIF(LAPACKE_ROOT_DIR) -+ SET(LAPACKE_INCLUDE_DIRS ${LAPACKE_INCLUDES}) -+ SET(LAPACKE_LIBRARIES ${LAPACKE_LIB} ${LAPACK_LIB}) -+ MARK_AS_ADVANCED(LAPACKE_INCLUDES LAPACKE_LIB LAPACK_LIB) - ENDIF(PC_LAPACKE_FOUND) - --IF(LAPACKE_LIB AND LAPACK_LIB) -- SET(LAPACK_LIBRARIES ${LAPACKE_LIB} ${LAPACK_LIB}) --ENDIF() --IF(LAPACKE_INCLUDES) -- SET(LAPACK_INCLUDE_DIR ${LAPACKE_INCLUDES}) --ENDIF() -- - INCLUDE(FindPackageHandleStandardArgs) --FIND_PACKAGE_HANDLE_STANDARD_ARGS(LAPACK DEFAULT_MSG -- LAPACK_INCLUDE_DIR LAPACK_LIBRARIES) -- --MARK_AS_ADVANCED(LAPACK_INCLUDES LAPACK_LIBRARIES) -+FIND_PACKAGE_HANDLE_STANDARD_ARGS(LAPACKE DEFAULT_MSG -+ LAPACKE_LIBRARIES -+ LAPACKE_INCLUDE_DIRS) -+MARK_AS_ADVANCED(LAPACKE_LIBRARIES -+ LAPACKE_INCLUDE_DIRS -+ LAPACKE_LIBRARY_DIRS) -diff --git a/src/backend/cpu/CMakeLists.txt b/src/backend/cpu/CMakeLists.txt -index ea57269..efe50a0 100644 ---- a/src/backend/cpu/CMakeLists.txt -+++ b/src/backend/cpu/CMakeLists.txt -@@ -55,7 +55,7 @@ MESSAGE(STATUS "FFTW Library: ${FFTW_LIBRARIES}") - - IF(APPLE) - FIND_PACKAGE(LAPACKE QUIET) # For finding MKL -- IF(NOT LAPACK_FOUND) -+ IF(NOT LAPACKE_FOUND) - # UNSET THE VARIABLES FROM LAPACKE - UNSET(LAPACKE_LIB CACHE) - UNSET(LAPACK_LIB CACHE) -@@ -67,11 +67,10 @@ ELSE(APPLE) # Linux and Windows - FIND_PACKAGE(LAPACKE) - ENDIF(APPLE) - --IF(NOT LAPACK_FOUND) -- MESSAGE(WARNING "LAPACK not found. Functionality will be disabled") --ELSE(NOT LAPACK_FOUND) -+IF(NOT LAPACKE_FOUND) -+ MESSAGE(WARNING "LAPACKE not found. Functionality will be disabled") -+ELSE(NOT LAPACKE_FOUND) - ADD_DEFINITIONS(-DWITH_CPU_LINEAR_ALGEBRA) -- MESSAGE(STATUS "LAPACK libraries found: ${LAPACK_LIBRARIES}") - ENDIF() - - IF(NOT UNIX) -@@ -99,8 +98,9 @@ INCLUDE_DIRECTORIES( - ${CBLAS_INCLUDE_DIR} - ) - --IF(LAPACK_FOUND) -- INCLUDE_DIRECTORIES(${LAPACK_INCLUDE_DIR}) -+IF(LAPACKE_FOUND) -+ INCLUDE_DIRECTORIES(${LAPACKE_INCLUDE_DIRS}) -+ LINK_DIRECTORIES(${LAPACKE_LIBRARY_DIRS}) - ENDIF() - - FILE(GLOB cpu_headers -@@ -213,8 +213,8 @@ IF(FORGE_FOUND AND NOT USE_SYSTEM_FORGE) - ADD_DEPENDENCIES(afcpu forge) - ENDIF() - --IF(LAPACK_FOUND) -- TARGET_LINK_LIBRARIES(afcpu PRIVATE ${LAPACK_LIBRARIES}) -+IF(LAPACKE_FOUND) -+ TARGET_LINK_LIBRARIES(afcpu PRIVATE ${LAPACKE_LIBRARIES}) - ENDIF() - - IF(FORGE_FOUND) -diff --git a/src/backend/cuda/CMakeLists.txt b/src/backend/cuda/CMakeLists.txt -index 4efb427..24c6544 100644 ---- a/src/backend/cuda/CMakeLists.txt -+++ b/src/backend/cuda/CMakeLists.txt -@@ -105,7 +105,7 @@ ELSE(CUDA_cusolver_LIBRARY) - ## Try to use CPU side lapack - IF(APPLE) - FIND_PACKAGE(LAPACKE QUIET) # For finding MKL -- IF(NOT LAPACK_FOUND) -+ IF(NOT LAPACKE_FOUND) - # UNSET THE VARIABLES FROM LAPACKE - UNSET(LAPACKE_LIB CACHE) - UNSET(LAPACK_LIB CACHE) -@@ -117,9 +117,9 @@ ELSE(CUDA_cusolver_LIBRARY) - FIND_PACKAGE(LAPACKE) - ENDIF(APPLE) - -- IF(NOT LAPACK_FOUND) -+ IF(NOT LAPACKE_FOUND) - MESSAGE(STATUS "CUDA Version ${CUDA_VERSION_STRING} does not contain cusolver library. Linear Algebra will not be available.") -- ELSE(NOT LAPACK_FOUND) -+ ELSE(NOT LAPACKE_FOUND) - MESSAGE(STATUS "CUDA Version ${CUDA_VERSION_STRING} does not contain cusolver library. But CPU LAPACK libraries are available. Will fallback to using host side code.") - ADD_DEFINITIONS(-DWITH_CPU_LINEAR_ALGEBRA) - IF(USE_CUDA_MKL) # Manual MKL Setup -@@ -148,7 +148,8 @@ INCLUDE_DIRECTORIES( - ) - - IF(CUDA_LAPACK_CPU_FALLBACK) -- INCLUDE_DIRECTORIES(${LAPACK_INCLUDE_DIR}) -+ INCLUDE_DIRECTORIES(${LAPACKE_INCLUDE_DIRS}) -+ LINK_DIRECTORIES(${LAPACKE_LIBRARY_DIRS}) - ENDIF() - - FILE(GLOB cuda_headers -@@ -379,7 +380,7 @@ ENDIF() - IF(CUDA_cusolver_LIBRARY) - TARGET_LINK_LIBRARIES(afcuda PRIVATE ${CUDA_cusolver_LIBRARY}) - ELSEIF(CUDA_LAPACK_CPU_FALLBACK) -- TARGET_LINK_LIBRARIES(afcuda PRIVATE ${LAPACK_LIBRARIES}) -+ TARGET_LINK_LIBRARIES(afcuda PRIVATE ${LAPACKE_LIBRARIES}) - ENDIF() - - SET_TARGET_PROPERTIES(afcuda PROPERTIES -diff --git a/src/backend/opencl/CMakeLists.txt b/src/backend/opencl/CMakeLists.txt -index 71247ce..ded53bf 100644 ---- a/src/backend/opencl/CMakeLists.txt -+++ b/src/backend/opencl/CMakeLists.txt -@@ -12,7 +12,7 @@ ENDIF() - - IF(APPLE) - FIND_PACKAGE(LAPACKE QUIET) # For finding MKL -- IF(NOT LAPACK_FOUND) -+ IF(NOT LAPACKE_FOUND) - # UNSET THE VARIABLES FROM LAPACKE - UNSET(LAPACKE_LIB CACHE) - UNSET(LAPACK_LIB CACHE) -@@ -24,9 +24,9 @@ ELSE(APPLE) # Linux and Windows - FIND_PACKAGE(LAPACKE) - ENDIF(APPLE) - --IF(NOT LAPACK_FOUND) -- MESSAGE(WARNING "LAPACK not found. Functionality will be disabled") --ELSE(NOT LAPACK_FOUND) -+IF(NOT LAPACKE_FOUND) -+ MESSAGE(WARNING "LAPACKE not found. Functionality will be disabled") -+ELSE(NOT LAPACKE_FOUND) - ADD_DEFINITIONS(-DWITH_OPENCL_LINEAR_ALGEBRA) - - IF(NOT USE_OPENCL_MKL) -@@ -105,8 +105,9 @@ INCLUDE_DIRECTORIES( - ${BoostCompute_INCLUDE_DIRS} - ${CBLAS_INCLUDE_DIR} - ) --IF(LAPACK_FOUND) -- INCLUDE_DIRECTORIES(${LAPACK_INCLUDE_DIR}) -+IF(LAPACKE_FOUND) -+ INCLUDE_DIRECTORIES(${LAPACKE_INCLUDE_DIRS}) -+ LINK_DIRECTORIES(${LAPACKE_LIBRARY_DIRS}) - ENDIF() - - FILE(GLOB opencl_headers -@@ -163,7 +164,7 @@ source_group(backend\\opencl\\kernel\\convolve\\Sources FILES ${conv_ker_sources - source_group(backend\\opencl\\cpu\\Headers FILES ${cpu_headers}) - source_group(backend\\opencl\\cpu\\Sources FILES ${cpu_sources}) - --IF(LAPACK_FOUND) -+IF(LAPACKE_FOUND) - FILE(GLOB magma_sources - "magma/*.cpp") - -@@ -313,9 +314,9 @@ IF(FORGE_FOUND AND NOT USE_SYSTEM_FORGE) - ADD_DEPENDENCIES(afopencl forge) - ENDIF() - --IF(LAPACK_FOUND) -+IF(LAPACKE_FOUND) - TARGET_LINK_LIBRARIES(afopencl -- PRIVATE ${LAPACK_LIBRARIES} -+ PRIVATE ${LAPACKE_LIBRARIES} - PRIVATE ${CBLAS_LIBRARIES}) - ENDIF() - diff --git a/gn/packages/patches/arrayfire-newer-boost-compute.patch b/gn/packages/patches/arrayfire-newer-boost-compute.patch deleted file mode 100644 index b08c121..0000000 --- a/gn/packages/patches/arrayfire-newer-boost-compute.patch +++ /dev/null @@ -1,33 +0,0 @@ -https://sources.debian.org/data/main/a/arrayfire/3.3.2+dfsg1-4/debian/patches/Use-compute-library-from-Boost-1.61.patch - -From: Ghislain Antony Vaillant <ghisvail@gmail.com> -Date: Fri, 12 Aug 2016 08:35:19 +0100 -Subject: Use compute library from Boost 1.61. - ---- - src/backend/opencl/CMakeLists.txt | 12 +++++++----- - 1 file changed, 7 insertions(+), 5 deletions(-) - -diff --git a/src/backend/opencl/CMakeLists.txt b/src/backend/opencl/CMakeLists.txt -index ded53bf..d7e3628 100644 ---- a/src/backend/opencl/CMakeLists.txt -+++ b/src/backend/opencl/CMakeLists.txt -@@ -84,11 +84,13 @@ ADD_DEFINITIONS( -DBOOST_ALL_NO_LIB ) - SET(Boost_USE_STATIC_LIBS OFF) - FIND_PACKAGE(Boost 1.48 REQUIRED) - --OPTION(USE_SYSTEM_BOOST_COMPUTE "Use system BoostCompute" OFF) --IF(USE_SYSTEM_BOOST_COMPUTE) -- FIND_PACKAGE(BoostCompute REQUIRED) --ELSE() -- INCLUDE("${CMAKE_MODULE_PATH}/build_boost_compute.cmake") -+IF(Boost_VERSION VERSION_LESS "1.61") -+ OPTION(USE_SYSTEM_BOOST_COMPUTE "Use system BoostCompute" OFF) -+ IF(USE_SYSTEM_BOOST_COMPUTE) -+ FIND_PACKAGE(BoostCompute REQUIRED) -+ ELSE() -+ INCLUDE("${CMAKE_MODULE_PATH}/build_boost_compute.cmake") -+ ENDIF() - ENDIF() - - SET( cl_kernel_headers diff --git a/gn/packages/patches/blist-stopiteration.patch b/gn/packages/patches/blist-stopiteration.patch deleted file mode 100644 index 198bef4..0000000 --- a/gn/packages/patches/blist-stopiteration.patch +++ /dev/null @@ -1,36 +0,0 @@ -From: Andrej Shadura <andrew.shadura@collabora.co.uk> -Date: Sun, 8 Jul 2018 09:00:16 +0200 -Subject: Catch StopIteration in a generator and return instead, per PEP 479 - -Signed-off-by: Andrej Shadura <andrew.shadura@collabora.co.uk> - -Forwarded: https://github.com/DanielStutzbach/blist/pull/92 -Bug-Debian: https://bugs.debian.org/902757 ---- - blist/_sortedlist.py | 13 ++++++++----- - 1 file changed, 8 insertions(+), 5 deletions(-) - -diff --git a/blist/_sortedlist.py b/blist/_sortedlist.py -index b34f69e..1f77170 100644 ---- a/blist/_sortedlist.py -+++ b/blist/_sortedlist.py -@@ -420,11 +420,14 @@ class _setmixin(object): - def __iter__(self): - it = super(_setmixin, self).__iter__() - while True: -- item = next(it) -- n = len(self) -- yield item -- if n != len(self): -- raise RuntimeError('Set changed size during iteration') -+ try: -+ item = next(it) -+ n = len(self) -+ yield item -+ if n != len(self): -+ raise RuntimeError('Set changed size during iteration') -+ except StopIteration: -+ return - - def safe_cmp(f): - def g(self, other): diff --git a/gn/packages/patches/delly-use-system-libraries.patch b/gn/packages/patches/delly-use-system-libraries.patch deleted file mode 100644 index 3ce817f..0000000 --- a/gn/packages/patches/delly-use-system-libraries.patch +++ /dev/null @@ -1,65 +0,0 @@ -This patch let's Delly use the system versions of htslib and boost. - -Patch by Roel Janssen <roel@gnu.org> ---- a/Makefile 2016-03-16 13:08:49.936706607 +0100 -+++ b/Makefile 2016-03-16 13:09:12.351706212 +0100 -@@ -9,8 +9,8 @@ - - # Flags - CXX=g++ --CXXFLAGS += -isystem ${SEQTK_ROOT} -isystem ${BOOST_ROOT} -pedantic -W -Wall -Wno-unknown-pragmas --LDFLAGS += -L${SEQTK_ROOT} -L${BOOST_ROOT}/stage/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time -+CXXFLAGS += -pedantic -W -Wall -Wno-unknown-pragmas -+LDFLAGS += -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time - - # Additional flags for release/debug - ifeq (${PARALLEL}, 1) -@@ -23,7 +23,7 @@ - ifeq (${STATIC}, 1) - LDFLAGS += -static -static-libgcc -pthread -lhts -lz - else -- LDFLAGS += -lhts -lz -Wl,-rpath,${SEQTK_ROOT},-rpath,${BOOST_ROOT}/stage/lib -+ LDFLAGS += -lhts -lz - endif - ifeq (${DEBUG}, 1) - CXXFLAGS += -g -O0 -fno-inline -DDEBUG -@@ -41,32 +41,24 @@ - DELLYSOURCES = $(wildcard src/*.h) $(wildcard src/*.cpp) - - # Targets --TARGETS = .htslib .boost src/delly src/extract src/cov src/iover src/stats -+TARGETS = src/delly src/extract src/cov src/iover src/stats - - all: $(TARGETS) - --.htslib: $(HTSLIBSOURCES) -- cd src/htslib && make && make lib-static && cd ../../ && touch .htslib -- --.boost: $(BOOSTSOURCES) -- cd src/modular-boost && ./bootstrap.sh --prefix=${PWD}/src/modular-boost --without-icu --with-libraries=iostreams,filesystem,system,program_options,date_time && ./b2 && ./b2 headers && cd ../../ && touch .boost -- --src/delly: .htslib .boost $(DELLYSOURCES) -+src/delly: $(DELLYSOURCES) - $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) - --src/extract: .htslib .boost $(DELLYSOURCES) -+src/extract: $(DELLYSOURCES) - $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) - --src/cov: .htslib .boost $(DELLYSOURCES) -+src/cov: $(DELLYSOURCES) - $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) - --src/iover: .htslib .boost $(DELLYSOURCES) -+src/iover: $(DELLYSOURCES) - $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) - --src/stats: .htslib .boost $(DELLYSOURCES) -+src/stats: $(DELLYSOURCES) - $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) - - clean: -- cd src/htslib && make clean -- cd src/modular-boost && ./b2 --clean-all -- rm -f $(TARGETS) $(TARGETS:=.o) .htslib .boost -+ rm -f $(TARGETS) $(TARGETS:=.o) diff --git a/gn/packages/patches/gnulib-gets.patch b/gn/packages/patches/gnulib-gets.patch deleted file mode 100644 index cccb55a..0000000 --- a/gn/packages/patches/gnulib-gets.patch +++ /dev/null @@ -1,60 +0,0 @@ -Minimally modified from upstream -only first change set from lib/stdio.in.h taken -s@lib/stdio@libgnu/stdio@g run on the 'diff' line. - -From: Eric Blake <eblake@redhat.com> -Date: Thu, 29 Mar 2012 19:30:41 +0000 (-0600) -Subject: stdio: don't assume gets any more -X-Git-Tag: v0.1~799 -X-Git-Url: https://git.savannah.gnu.org/gitweb/?p=gnulib.git;a=commitdiff_plain;h=66712c23388e93e5c518ebc8515140fa0c807348 - -stdio: don't assume gets any more - -Gnulib intentionally does not have a gets module, and now that C11 -and glibc have dropped it, we should be more proactive about warning -any user on a platform that still has a declaration of this dangerous -interface. - -* m4/stdio_h.m4 (gl_STDIO_H, gl_STDIO_H_DEFAULTS): Drop gets -support. -* modules/stdio (Makefile.am): Likewise. -* gnu/stdio-read.c (gets): Likewise. -* tests/test-stdio-c++.cc: Likewise. -* m4/warn-on-use.m4 (gl_WARN_ON_USE_PREPARE): Fix comment. -* gnu/stdio.in.h (gets): Make warning occur in more places. -* doc/posix-functions/gets.texi (gets): Update documentation. -Reported by Christer Solskogen. - -Signed-off-by: Eric Blake <eblake@redhat.com> ---- -diff --git a/libgnu/stdio.in.h b/libgnu/stdio.in.h -index aa7b599..c377b6e 100644 ---- a/libgnu/stdio.in.h -+++ b/libgnu/stdio.in.h -@@ -698,22 +698,11 @@ _GL_WARN_ON_USE (getline, "getline is unportable - " - # endif - #endif - --#if @GNULIB_GETS@ --# if @REPLACE_STDIO_READ_FUNCS@ && @GNULIB_STDIO_H_NONBLOCKING@ --# if !(defined __cplusplus && defined GNULIB_NAMESPACE) --# undef gets --# define gets rpl_gets --# endif --_GL_FUNCDECL_RPL (gets, char *, (char *s) _GL_ARG_NONNULL ((1))); --_GL_CXXALIAS_RPL (gets, char *, (char *s)); --# else --_GL_CXXALIAS_SYS (gets, char *, (char *s)); --# undef gets --# endif --_GL_CXXALIASWARN (gets); - /* It is very rare that the developer ever has full control of stdin, -- so any use of gets warrants an unconditional warning. Assume it is -- always declared, since it is required by C89. */ -+ so any use of gets warrants an unconditional warning; besides, C11 -+ removed it. */ -+#undef gets -+#if HAVE_RAW_DECL_GETS - _GL_WARN_ON_USE (gets, "gets is a security hole - use fgets instead"); - #endif - diff --git a/gn/packages/patches/octave-nested-class.patch b/gn/packages/patches/octave-nested-class.patch deleted file mode 100644 index 6d835cb..0000000 --- a/gn/packages/patches/octave-nested-class.patch +++ /dev/null @@ -1,39 +0,0 @@ -https://hg.savannah.gnu.org/hgweb/octave/raw-rev/7ffd2a0791ef - -# HG changeset patch -# User John W. Eaton <jwe@octave.org> -# Date 1325958274 18000 -# Node ID 7ffd2a0791ef389474bb52228e9b046a3721ab3f -# Parent 906eecd4bf43b0146c50019ee41acac2dc83c935 -fix name lookup problem with static nested class - -* oct-inttypes.h (octave_int_arith_base<T,false>::mul): -Tag truncate_int with octave_int_base<T>::. -(octave_int_arith_base<T,true>::mul): Likewise. - -diff --git a/liboctave/oct-inttypes.h b/liboctave/oct-inttypes.h ---- a/liboctave/oct-inttypes.h -+++ b/liboctave/oct-inttypes.h -@@ -366,8 +366,8 @@ - { - // Promotion type for multiplication (if exists). - typedef typename query_integer_type<2*sizeof (T), false>::type mptype; -- return truncate_int (static_cast<mptype> (x) -- * static_cast<mptype> (y)); -+ return octave_int_base<T>::truncate_int (static_cast<mptype> (x) -+ * static_cast<mptype> (y)); - } - - // Division with rounding to nearest. Note that / and % are probably -@@ -621,8 +621,8 @@ - { - // Promotion type for multiplication (if exists). - typedef typename query_integer_type<2*sizeof (T), true>::type mptype; -- return truncate_int (static_cast<mptype> (x) -- * static_cast<mptype> (y)); -+ return octave_int_base<T>::truncate_int (static_cast<mptype> (x) -+ * static_cast<mptype> (y)); - } - - // Division. - diff --git a/gn/packages/patches/plink-ng-Makefile-zlib.patch b/gn/packages/patches/plink-ng-Makefile-zlib.patch deleted file mode 100644 index f3bb269..0000000 --- a/gn/packages/patches/plink-ng-Makefile-zlib.patch +++ /dev/null @@ -1,126 +0,0 @@ -diff --git a/Makefile.std b/Makefile.std -index 95b0940..30206be 100644 ---- a/Makefile.std -+++ b/Makefile.std -@@ -1,62 +1,22 @@ - # General-purpose Makefile for PLINK 1.90 - # --# Compilation options: --# Do not link to LAPACK NO_LAPACK - --# Leave blank after "=" to disable; put "= 1" to enable --# (when enabled, "#define NOLAPACK" must be uncommented in plink_common.h) --NO_LAPACK = -- -- --# should autodetect system --SYS = UNIX --ifdef SystemRoot -- SYS = WIN --else -- UNAME := $(shell uname) -- ifeq ($(UNAME), Darwin) -- SYS = MAC -- endif --endif -- --CFLAGS=-Wall -O2 --BLASFLAGS=-L/usr/lib64/atlas -llapack -lcblas -latlas --LINKFLAGS=-lm -lpthread --ZLIB=zlib-1.2.8/libz.so.1.2.8 -- --ifeq ($(SYS), MAC) -- GCC_GTEQ_43 := $(shell expr `g++ -dumpversion | sed -e 's/\.\([0-9][0-9]\)/\1/g' -e 's/\.\([0-9]\)/0\1/g' -e 's/^[0-9]\{3,4\}$$/&00/'` \>= 40300) -- ifeq "$(GCC_GTEQ_43)" "1" -- CFLAGS=-Wall -O2 -flax-vector-conversions -- endif -- BLASFLAGS=-framework Accelerate -- LINKFLAGS= -- ZLIB=zlib-1.2.8/libz.1.2.8.dylib --endif -- --ifeq ($(SYS), WIN) --# Note that, unlike the Linux and Mac build processes, this STATICALLY links --# LAPACK, since we have not gotten around to trying dynamically-linked LAPACK --# on Windows. --# If you don't already have LAPACK built, you'll probably want to turn on --# NO_LAPACK. -- BLASFLAGS=-L. lapack/liblapack.a -L. lapack/librefblas.a -- LINKFLAGS=-lm -static-libgcc -- ZLIB=zlib-1.2.8/libz.a --endif -- --ifdef NO_LAPACK -- BLASFLAGS= --endif -+# CFLAGS=-Wall -O2 -+# BLASFLAGS=-lblas -llapack -latlas -+LINKFLAGS=-lm -lpthread -lopenblas -llapack -latlas -lstdc++ -+ZLIB=-lz - - SRC = plink.c plink_assoc.c plink_calc.c plink_cluster.c plink_cnv.c plink_common.c plink_data.c plink_dosage.c plink_family.c plink_filter.c plink_glm.c plink_help.c plink_homozyg.c plink_lasso.c plink_ld.c plink_matrix.c plink_misc.c plink_set.c plink_stats.c SFMT.c dcdflib.c pigz.c yarn.c - -+OBJ = plink.o plink_assoc.o plink_calc.o plink_cluster.o plink_cnv.o plink_common.o plink_data.o plink_dosage.o plink_family.o plink_filter.o plink_glm.o plink_help.o plink_homozyg.o plink_lasso.o plink_ld.o plink_matrix.o plink_misc.o plink_set.o plink_stats.o SFMT.o dcdflib.o pigz.o yarn.o -+ - # In the likely event that you are concurrently using PLINK 1.07, we suggest - # either renaming that binary to "plink1" or this one to "plink2". - --plink: $(SRC) -- g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB) -+# plink: $(SRC) -+# g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB) - --plinkw: $(SRC) -+plink: $(SRC) - g++ $(CFLAGS) $(SRC) -c -- gfortran -O2 $(OBJ) -o plink -Wl,-Bstatic $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB) -+ gfortran $(OBJ) -o plink2 $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB) -+ # gfortran $^ -o plink2 -Wl,-Bstatic $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB) -diff --git a/dose2plink.c b/dose2plink.c -index dc1f33a..ca2d31c 100644 ---- a/dose2plink.c -+++ b/dose2plink.c -@@ -96,7 +96,7 @@ - #endif - #endif - --#include "zlib-1.2.8/zlib.h" -+#include "zlib.h" - - #ifdef __APPLE__ - #include <sys/sysctl.h> -diff --git a/pigz.c b/pigz.c -index 6605925..3f4ca54 100644 ---- a/pigz.c -+++ b/pigz.c -@@ -303,7 +303,7 @@ - #include <stdio.h> - #include <stdlib.h> - #include <windows.h> --#include "zlib-1.2.8/zlib.h" -+#include "zlib.h" - - void pigz_init(uint32_t setprocs) { - return; -@@ -383,7 +383,7 @@ void parallel_compress(char* out_fname, uint32_t do_append, uint32_t(* emitn)(ui - # include <sys/pstat.h> - #endif - --#include "zlib-1.2.8/zlib.h" /* deflateInit2(), deflateReset(), deflate(), */ -+#include "zlib.h" /* deflateInit2(), deflateReset(), deflate(), */ - /* deflateEnd(), deflateSetDictionary(), crc32(), - inflateBackInit(), inflateBack(), inflateBackEnd(), - Z_DEFAULT_COMPRESSION, Z_DEFAULT_STRATEGY, -diff --git a/plink_common.h b/plink_common.h -index 5dd77e8..4da9371 100644 ---- a/plink_common.h -+++ b/plink_common.h -@@ -139,7 +139,7 @@ - - #endif // __LP64__ - --#include "zlib-1.2.8/zlib.h" -+#include "zlib.h" - #include "SFMT.h" - - // 64MB of non-workspace memory guaranteed for now diff --git a/gn/packages/patches/python-twint-mentions.patch b/gn/packages/patches/python-twint-mentions.patch deleted file mode 100644 index f792786..0000000 --- a/gn/packages/patches/python-twint-mentions.patch +++ /dev/null @@ -1,16 +0,0 @@ -diff --git a/twint/format.py b/twint/format.py -index 334b43a..3eeb8c2 100644 ---- a/twint/format.py -+++ b/twint/format.py -@@ -29,7 +29,10 @@ def Tweet(config, t): - output = output.replace("{quote_url}", t.quote_url) - output = output.replace("{near}", t.near) - output = output.replace("{geo}", t.geo) -- output = output.replace("{mentions}", ",".join(t.mentions)) -+ output = output.replace("{mentions}", -+ ",".join(map(lambda x: x.get("screen_name", -+ None), -+ t.mentions))) - output = output.replace("{translate}", t.translate) - output = output.replace("{trans_src}", t.trans_src) - output = output.replace("{trans_dest}", t.trans_dest) diff --git a/gn/packages/patches/python-twint-token.patch b/gn/packages/patches/python-twint-token.patch deleted file mode 100644 index 570ca8b..0000000 --- a/gn/packages/patches/python-twint-token.patch +++ /dev/null @@ -1,11 +0,0 @@ -diff --git a/twint/token.py b/twint/token.py -index 0eeb0dc..63b637a 100644 ---- a/twint/token.py -+++ b/twint/token.py -@@ -20,0 +21,6 @@ class Token: -+ self._session.headers.update( -+ {'User-Agent': -+ ('Mozilla/5.0 ' -+ '(Windows NT 10.0;' -+ ' Win64; x64; rv:78.0)' -+ ' Gecko/20100101 Firefox/78.0')}) diff --git a/gn/packages/patches/python-twint-userlist.patch b/gn/packages/patches/python-twint-userlist.patch deleted file mode 100644 index 1d5b860..0000000 --- a/gn/packages/patches/python-twint-userlist.patch +++ /dev/null @@ -1,19 +0,0 @@ -diff --git a/twint/cli.py b/twint/cli.py -index f463d68..68244c9 100644 ---- a/twint/cli.py -+++ b/twint/cli.py -@@ -69,10 +69,10 @@ def loadUserList(ul, _type): - else: - userlist = ul.split(",") - if _type == "search": -- un = "" -- for user in userlist: -- un += "%20OR%20from%3A" + user -- return un[15:] -+ un = userlist[0] -+ for user in userlist[1:]: -+ un += " OR from:" + user -+ return un - return userlist - - diff --git a/gn/packages/patches/python-unittest2-python3-compat.patch b/gn/packages/patches/python-unittest2-python3-compat.patch deleted file mode 100644 index 68fbcca..0000000 --- a/gn/packages/patches/python-unittest2-python3-compat.patch +++ /dev/null @@ -1,46 +0,0 @@ -Skip tests that fail with newer versions of Python. - -Patch copied from Gentoo: - -https://gitweb.gentoo.org/repo/gentoo.git/tree/dev-python/unittest2/files/unittest2-1.1.0-python3.5-test.patch - -diff --git a/unittest2/test/test_loader.py b/unittest2/test/test_loader.py -index 683f662..347eea5 100644 ---- a/unittest2/test/test_loader.py -+++ b/unittest2/test/test_loader.py -@@ -509,6 +509,7 @@ class Test_TestLoader(unittest2.TestCase): - # - # What happens when an impossible name is given, relative to the provided - # `module`? -+ @unittest.skipIf(sys.version_info[:2] >= (3, 5), "python 3.5 has problems here") - def test_loadTestsFromName__relative_malformed_name(self): - loader = unittest.TestLoader() - -@@ -811,6 +812,7 @@ class Test_TestLoader(unittest2.TestCase): - # TestCase or TestSuite instance." - # - # What happens when presented with an impossible module name? -+ @unittest.skipIf(sys.version_info[:2] >= (3, 5), "python 3.5 has problems here") - def test_loadTestsFromNames__malformed_name(self): - loader = unittest2.TestLoader() - -@@ -918,6 +920,7 @@ class Test_TestLoader(unittest2.TestCase): - # "The method optionally resolves name relative to the given module" - # - # What happens when presented with an impossible attribute name? -+ @unittest.skipIf(sys.version_info[:2] >= (3, 5), "python 3.5 has problems here") - def test_loadTestsFromNames__relative_malformed_name(self): - loader = unittest.TestLoader() - -diff --git a/unittest2/compatibility.py b/unittest2/compatibility.py -index 9e5f1a5..2d20c19 100644 ---- a/unittest2/compatibility.py -+++ b/unittest2/compatibility.py -@@ -140,6 +140,6 @@ except ImportError: - ### ChainMap (helper for configparser and string.Template) - ######################################################################## - --class ChainMap(collections.MutableMapping): -+class ChainMap(collections.abc.MutableMapping): - ''' A ChainMap groups multiple dicts (or other mappings) together - to create a single, updateable view. diff --git a/gn/packages/patches/python-unittest2-remove-argparse.patch b/gn/packages/patches/python-unittest2-remove-argparse.patch deleted file mode 100644 index c967387..0000000 --- a/gn/packages/patches/python-unittest2-remove-argparse.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/setup.py 2017-09-12 01:22:06.273997788 +0200 -+++ b/setup.py 2017-09-12 01:22:14.297918757 +0200 -@@ -57,7 +57,7 @@ - # Both install and setup requires - because we read VERSION from within the - # package, and the package also exports all the APIs. - # six for compat helpers --REQUIRES = ['argparse', 'six>=1.4', 'traceback2'], -+REQUIRES = ['six>=1.4', 'traceback2'], - - params = dict( - name=NAME, diff --git a/gn/packages/patches/python2-htmlgen-Applied-Deb-patch.patch b/gn/packages/patches/python2-htmlgen-Applied-Deb-patch.patch deleted file mode 100644 index d6a957c..0000000 --- a/gn/packages/patches/python2-htmlgen-Applied-Deb-patch.patch +++ /dev/null @@ -1,263 +0,0 @@ -From c0b16bbad9b8e396bdb64c638a3540547acfa3a5 Mon Sep 17 00:00:00 2001 -From: Pjotr Prins <pjotr.public01@thebird.nl> -Date: Sat, 13 Feb 2016 13:39:03 +0100 -Subject: [PATCH 1/2] Applied Deb patch - ---- - Formtools.py | 1 - - HTMLcalendar.py | 9 ++++----- - HTMLgen.py | 6 +++--- - HTMLtest.py | 12 ++++++------ - HTMLutil.py | 19 +++++++++---------- - ImagePaletteH.py | 2 +- - Makefile | 10 ++++++++++ - NavLinks.py | 1 - - barchart.py | 1 - - colorcube.py | 1 - - 10 files changed, 33 insertions(+), 29 deletions(-) - -diff --git a/Formtools.py b/Formtools.py -index bb598f4..1dabccd 100644 ---- a/Formtools.py -+++ b/Formtools.py -@@ -1,4 +1,3 @@ --#! /usr/bin/env python - "Provide some supporting classes to simplify Input Forms with HTMLgen" - #'$Id: Formtools.py,v 1.1 1999/04/19 23:45:36 friedric Exp friedric $' - # COPYRIGHT (C) 1999 ROBIN FRIEDRICH email: Robin.Friedrich@pdq.net -diff --git a/HTMLcalendar.py b/HTMLcalendar.py -index 3a03915..35edf27 100644 ---- a/HTMLcalendar.py -+++ b/HTMLcalendar.py -@@ -1,4 +1,3 @@ --#!/usr/bin/env python - # COPYRIGHT (C) 1997 ROBIN FRIEDRICH - # Permission to use, copy, modify, and distribute this software and its - # documentation for any purpose and without fee is hereby granted, -@@ -212,12 +211,12 @@ def makeint(value): - return value - else: - raise TypeError, ('cannot convert to int', value) --import regex --datepat = regex.compile('^ *\([0-9*][0-9]?\)[/-]' #first 2 char date field -+import re -+datepat = re.compile('^ *\([0-9*][0-9]?\)[/-]' #first 2 char date field - '\([0-9][0-9]?\)[/-]?' #second 2 char date field - '\([12][0-9][0-9][0-9]\)?[ \t]*:') #optional year field --daypat = regex.compile('^ *\('+string.join(day_name,'\|')+'\)') --timepat = regex.compile('\([0-9][0-9]?\):\([0-9][0-9]\)') -+daypat = re.compile('^ *\('+string.join(day_name,'\|')+'\)') -+timepat = re.compile('\([0-9][0-9]?\):\([0-9][0-9]\)') - - def read_appt_file(filename): - """Parsing function. -diff --git a/HTMLgen.py b/HTMLgen.py -index 10ecd28..dbdbd81 100644 ---- a/HTMLgen.py -+++ b/HTMLgen.py -@@ -284,7 +284,7 @@ class SimpleDocument(BasicDocument): - if self.meta: s.append(str(self.meta)) - if self.base: s.append(str(self.base)) - if self.stylesheet: -- s.append('\n <LINK rel=stylesheet href="%s" type=text/css title="%s">\n' \ -+ s.append('\n <LINK rel=stylesheet href="%s" type="text/css" title="%s">\n' \ - % (self.stylesheet, self.stylesheet)) - if self.style: - s.append('\n<STYLE>\n<!--\n%s\n-->\n</style>\n' % self.style) -@@ -1083,7 +1083,7 @@ class List(UserList.UserList): - - Overloaded by child classes to represent other list styles. - """ -- return '%s<LI>%s\n' % (self.pad*self.lvl, item) -+ return '%s<LI>%s</LI>\n' % (self.pad*self.lvl, item) - - def start_element(self): - """Generic creator for the HTML element opening tag. -@@ -2463,7 +2463,7 @@ class URL: - import urlparse - self.unparse = urlparse.urlunparse - self.proto, self.node, self.path, self.params, self.query, self.fragment = \ -- urlparse(url) -+ urlparse.urlparse(url) - self.dir, self.file = self.split(self.path) - - def split(self, p): -diff --git a/HTMLtest.py b/HTMLtest.py -index 5850a04..283233f 100755 ---- a/HTMLtest.py -+++ b/HTMLtest.py -@@ -1,8 +1,8 @@ --#!/bin/env python -+#!/usr/bin/env python - - """Test script which generates the online documentation for HTMLgen. - """ --import string, regex, regsub, os, time, glob -+import string, re, os, time, glob - from HTMLcolors import * - from HTMLgen import * - import HTMLgen #only so I can pick off the __version__ -@@ -232,11 +232,11 @@ def sample1(filename, aft=None, fore=None, top=None, home=None): - doc.email = 'jefferson@montecello.virginia.gov' - doc.logo = ('../image/eagle21.gif', 64, 54) - # parse Declaration of Independence -- re_hline = regex.compile('^--+$') -- re_title = regex.compile('^Title:\(.*$\)') -+ re_hline = re.compile('^--+$') -+ re_title = re.compile('^Title:\(.*$\)') - font2 = Font(size='+2') - s = open(os.path.join(datadir, 'DoI.txt')).read() -- paragraphs = regsub.split(s, '\n\([\t ]*\n\)+') -+ paragraphs = re.split(s, '\n\([\t ]*\n\)+') - for para in paragraphs: - if not para: continue - if re_title.search(para) > -1: -@@ -263,7 +263,7 @@ def sample2(filename, aft=None, fore=None, top=None, home=None): - #Ok parse that file - f = open(mpath(os.path.join(datadir, 'parrot.txt'))) - line = f.readline() -- re_dialog = regex.compile('\(^[OC].*:\)\(.*\)') -+ re_dialog = re.compile('\(^[OC].*:\)\(.*\)') - while line: - if re_dialog.search(line) > -1: - role, prose = re_dialog.group(1,2) -diff --git a/HTMLutil.py b/HTMLutil.py -index 2baf168..9a877e5 100755 ---- a/HTMLutil.py -+++ b/HTMLutil.py -@@ -1,4 +1,3 @@ --#!/usr/bin/env python - """This module provides utility functions/classes associated with HTMLgen. - - This is functionality use by HTMLgen script writers rather than by HTMLgen -@@ -19,7 +18,7 @@ itself. (i.e. HTMLgen.py is not dependant on this module.) - # OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR - # PERFORMANCE OF THIS SOFTWARE. - __version__ = '$Id: HTMLutil.py,v 1.3 1998/05/28 20:14:52 friedric Exp $' --import string, regex, os -+import string, re, os - import HTMLgen, HTMLcolors - from types import * - -@@ -79,7 +78,7 @@ def been_marked(text): - """Determine if the text have been marked by a previous gsub. - (ugly hack but it works) - """ -- if regex.search('\(</?FONT\)\|\(</?STRONG\)', text) > -1: -+ if re.search('\(</?FONT\)\|\(</?STRONG\)', text) > -1: - return 1 - else: - return 0 -@@ -125,13 +124,13 @@ def global_substitute(search_func, repl_func, s): - not_backslash = "[^\\\\]" - triple_single = "'''" - triple_double = '"""' --_doc_start_re = regex.compile( -+_doc_start_re = re.compile( - "\(^\|" + not_backslash + "\)" # bol or not backslash - + "\(" + triple_single + "\|" + triple_double + "\)" ) - single_re = not_backslash + triple_single - double_re = not_backslash + triple_double --_triple_re = { triple_single : regex.compile(single_re), -- triple_double : regex.compile(double_re) } -+_triple_re = { triple_single : re.compile(single_re), -+ triple_double : re.compile(double_re) } - - del not_backslash, triple_single, triple_double, \ - single_re, double_re -@@ -150,13 +149,13 @@ def find_docstring( s, begin=0): - return (None, None) - return startquote, quotefinder.regs[0][1] - --string_re = regex.compile('\(\(\'[^\'\n]*\'\)\|\("[^"\n]"\)\)') -+string_re = re.compile('\(\(\'[^\'\n]*\'\)\|\("[^"\n]"\)\)') - def find_string_literal( s, begin=0 ): - if string_re.search(s, begin) > -1: - return string_re.regs[1] - return (None, None) - --comment_re = regex.compile('#.*$') -+comment_re = re.compile('#.*$') - def find_comment( s, begin=0 ): - while comment_re.search(s, begin) > -1: - if been_marked(comment_re.group(0)): -@@ -166,13 +165,13 @@ def find_comment( s, begin=0 ): - return (None, None) - - Name = '[a-zA-Z_][a-zA-Z0-9_]*' --func_re = regex.compile('\(^[ \t]*def[ \t]+' +Name+ '\)[ \t]*(') -+func_re = re.compile('\(^[ \t]*def[ \t]+' +Name+ '\)[ \t]*(') - def find_function( s, begin=0 ): - if func_re.search(s, begin) > -1: - return func_re.regs[1] - return (None, None) - --class_re = regex.compile('\(^[ \t]*class[ \t]+' +Name+ '\)[ \t]*[(:]') -+class_re = re.compile('\(^[ \t]*class[ \t]+' +Name+ '\)[ \t]*[(:]') - def find_class( s, begin=0 ): - if class_re.search(s, begin) > -1: - return class_re.regs[1] -diff --git a/ImagePaletteH.py b/ImagePaletteH.py -index 83bb867..e723847 100644 ---- a/ImagePaletteH.py -+++ b/ImagePaletteH.py -@@ -70,7 +70,7 @@ def negative(mode = "RGB"): - return ImagePalette(mode, palette * len(mode)) - - def random(mode = "RGB"): -- from whrandom import randint -+# from whrandom import randint - palette = map(lambda a: randint(0, 255), [0]*256*len(mode)) - return ImagePalette(mode, palette) - -diff --git a/Makefile b/Makefile -index 1788fa6..e1ec846 100644 ---- a/Makefile -+++ b/Makefile -@@ -62,6 +62,16 @@ install: compileall - python installp.py -f $(MODULES) $(MODULESC) $(PIL) $(PILC) - @echo Installation of $(PACKAGE) done. - -+debinstall: -+ if [ -z "$(PYLIBDIR)" ]; then \ -+ echo "Unset PYLIBDIR."; \ -+ exit 1; \ -+ fi; \ -+ for f in $(MODULES) $(PIL); do \ -+ install -m 644 $$f $(PYLIBDIR)/; \ -+ done -+ @echo Installation of $(PACKAGE) done. -+ - checkin: - ci -u $(MODULES) $(PIL) $(EXTRAS) $(TEST) Makefile - -diff --git a/NavLinks.py b/NavLinks.py -index fcecbb3..51ef774 100644 ---- a/NavLinks.py -+++ b/NavLinks.py -@@ -1,4 +1,3 @@ --#!/usr/bin/env python - #'$Id: NavLinks.py,v 1.1 1999/02/04 04:54:29 friedric Exp friedric $' - # COPYRIGHT (C) 1999 ROBIN FRIEDRICH email:Robin.Friedrich@pdq.net - # Permission to use, copy, modify, and distribute this software and -diff --git a/barchart.py b/barchart.py -index 882cde5..a901fe4 100755 ---- a/barchart.py -+++ b/barchart.py -@@ -1,4 +1,3 @@ --#!/usr/bin/env python - - """Provides BarChart class which creates HTML 1D bar charts, - and StackedBarChart class to deal with multiple data plotting -diff --git a/colorcube.py b/colorcube.py -index be91154..94fa7dd 100644 ---- a/colorcube.py -+++ b/colorcube.py -@@ -1,4 +1,3 @@ --#!/usr/bin/env python - - """Utility to generate a table of browser safe colors. - """ --- -2.1.4 - diff --git a/gn/packages/patches/python2-htmlgen-Fix-test-for-random.patch b/gn/packages/patches/python2-htmlgen-Fix-test-for-random.patch deleted file mode 100644 index 279a82f..0000000 --- a/gn/packages/patches/python2-htmlgen-Fix-test-for-random.patch +++ /dev/null @@ -1,25 +0,0 @@ -From c9ca65d39ca1185cebf5be86a10ba0ceea171249 Mon Sep 17 00:00:00 2001 -From: Pjotr Prins <pjotr.public01@thebird.nl> -Date: Sat, 13 Feb 2016 13:40:46 +0100 -Subject: [PATCH 2/2] Fix test for random - ---- - HTMLgen.py | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/HTMLgen.py b/HTMLgen.py -index dbdbd81..034f672 100644 ---- a/HTMLgen.py -+++ b/HTMLgen.py -@@ -924,7 +924,7 @@ class MailTo: - def antispam(self, address): - """Process a string with HTML encodings to defeat address spiders. - """ -- from whrandom import choice -+ from random import choice - buffer = map(None, address) - for i in range(0, len(address), choice((2,3,4))): - buffer[i] = '&#%d;' % ord(buffer[i]) --- -2.1.4 - diff --git a/gn/packages/patches/quast.patch b/gn/packages/patches/quast.patch deleted file mode 100644 index 31e5460..0000000 --- a/gn/packages/patches/quast.patch +++ /dev/null @@ -1,88 +0,0 @@ -This patch is mostly adapted from the Debian patches -https://salsa.debian.org/med-team/quast/-/tree/master/debian/patches - -diff --git a/setup.py b/setup.py -index a982a430..24ab2f5f 100755 ---- a/setup.py -+++ b/setup.py -@@ -35,10 +35,10 @@ except: - exit_with_code=1) - - from quast_libs.glimmer import compile_glimmer --from quast_libs.run_busco import download_augustus, download_all_db --from quast_libs.search_references_meta import download_blast_binaries, download_blastdb -+from quast_libs.run_busco import download_all_db -+from quast_libs.search_references_meta import download_blastdb - from quast_libs.ca_utils.misc import compile_aligner --from quast_libs.ra_utils.misc import compile_reads_analyzer_tools, compile_bwa, compile_bedtools, download_gridss -+from quast_libs.ra_utils.misc import compile_reads_analyzer_tools, download_gridss - - name = 'quast' - quast_package = qconfig.PACKAGE_NAME -@@ -60,8 +60,6 @@ if cmd_in(['clean', 'sdist']): - logger.info('Cleaning up binary files...') - compile_aligner(logger, only_clean=True) - compile_glimmer(logger, only_clean=True) -- compile_bwa(logger, only_clean=True) -- compile_bedtools(logger, only_clean=True) - for fpath in [fn for fn in glob(join(quast_package, '*.pyc'))]: os.remove(fpath) - for fpath in [fn for fn in glob(join(quast_package, 'html_saver', '*.pyc'))]: os.remove(fpath) - for fpath in [fn for fn in glob(join(quast_package, 'site_packages', '*', '*.pyc'))]: os.remove(fpath) -@@ -74,10 +72,7 @@ if cmd_in(['clean', 'sdist']): - if isdir(name + '.egg-info'): - shutil.rmtree(name + '.egg-info') - download_gridss(logger, only_clean=True) -- download_blast_binaries(logger, only_clean=True) -- download_blastdb(logger, only_clean=True) - if qconfig.platform_name != 'macosx': -- download_augustus(logger, only_clean=True) - download_all_db(logger, only_clean=True) - logger.info('Done.') - sys.exit() -@@ -168,9 +163,6 @@ if cmd_in(['install', 'develop', 'build', 'build_ext']): - logger.info('* Downloading GRIDSS *') - if not download_gridss(logger): - modules_failed_to_install.append('GRIDSS (affects -1/--reads1 and -2/--reads2 options)') -- logger.info('* Downloading BLAST *') -- if not download_blast_binaries(logger): -- modules_failed_to_install.append('BLAST (affects metaquast.py in without references mode and --find-conserved-genes option)') - logger.info('* Downloading SILVA 16S rRNA gene database *') - if not download_blastdb(logger): - modules_failed_to_install.append('SILVA 16S rRNA gene database (affects metaquast.py in without references mode)') -@@ -186,20 +178,8 @@ if cmd_in(['install', 'develop', 'build', 'build_ext']): - logger.info('') - - --if qconfig.platform_name == 'macosx': -- sambamba_files = [join('sambamba', 'sambamba_osx')] --else: -- sambamba_files = [join('sambamba', 'sambamba_linux')] -- --minimap_files = find_package_files('minimap2') --bwa_files = [ -- join('bwa', fp) for fp in os.listdir(join(quast_package, 'bwa')) -- if isfile(join(quast_package, 'bwa', fp)) and fp.startswith('bwa')] --bedtools_files = [join('bedtools', 'bin', '*')] - full_install_tools = ( -- find_package_files('gridss') + -- find_package_files('blast') + -- [join(quast_package, 'busco', 'hmmsearch')] -+ find_package_files('gridss') - ) - - setup( -@@ -229,14 +209,10 @@ The tool accepts multiple assemblies, thus is suitable for comparison.''', - 'manual.html', - ] + - find_package_files('html_saver') + -- minimap_files + - find_package_files('genemark/' + qconfig.platform_name) + - find_package_files('genemark-es/' + qconfig.platform_name) + - find_package_files('genemark-es/lib') + - find_package_files('glimmer') + -- bwa_files + -- bedtools_files + -- sambamba_files + - (full_install_tools if install_full else []) - }, - include_package_data=True, diff --git a/gn/packages/patches/vcflib-use-system-fastahack-smithwaterman.patch b/gn/packages/patches/vcflib-use-system-fastahack-smithwaterman.patch deleted file mode 100644 index 91f372c..0000000 --- a/gn/packages/patches/vcflib-use-system-fastahack-smithwaterman.patch +++ /dev/null @@ -1,107 +0,0 @@ -diff --git a/CMakeLists.txt b/CMakeLists.txt -index af3fe67..f237563 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -63,8 +63,10 @@ set_package_properties(ZLIB PROPERTIES TYPE REQUIRED) - find_package(Threads) - set_package_properties(Threads PROPERTIES TYPE REQUIRED) - --pkg_check_modules(htslib IMPORTED_TARGET htslib) # Optionally builds from contrib/ --pkg_check_modules(tabixpp IMPORTED_TARGET tabixpp) # Optionally builds from contrib/ -+pkg_check_modules(htslib IMPORTED_TARGET htslib) # Optionally builds from contrib/ -+pkg_check_modules(tabixpp IMPORTED_TARGET tabixpp) # Optionally builds from contrib/ -+pkg_check_modules(fastahack IMPORTED_TARGET fastahack) # Optionally builds from contrib/ -+pkg_check_modules(smithwaterman IMPORTED_TARGET smithwaterman) # Optionally builds from contrib/ - - # ---- Build switches - set(CMAKE_INTERPROCEDURAL_OPTIMIZATION ${ipo_supported}) -@@ -113,12 +115,20 @@ endif(ZIG) - # ---- Include files - - include_directories(include) --include_directories(contrib/fastahack) - include_directories(contrib/intervaltree) --include_directories(contrib/smithwaterman) - include_directories(contrib/filevercmp) - include_directories(contrib/c-progress-bar) - -+if(NOT fastahack_FOUND) -+ message(STATUS "Using included fastahack") -+ include_directories(contrib/fastahack) -+endif() -+ -+if(NOT smithwaterman_FOUND) -+ message(STATUS "Using included smithwaterman") -+ include_directories(contrib/smithwaterman) -+endif() -+ - if(NOT htslib_FOUND) - message(STATUS "Using included htslib") - include(FindCURL) # for htslib -@@ -142,11 +152,19 @@ endif() - file(GLOB INCLUDES - src/*.h* - contrib/intervaltree/*.h* -- contrib/smithwaterman/*.h* -- contrib/fastahack/*.h* - contrib/filevercmp/*.h* - ) - -+if(NOT fastahack_FOUND) -+ file(GLOB FASTAHACK_INCLUDES contrib/fastahack/*.h*) -+ list(APPEND INCLUDES ${FASTAHACK_INCLUDES}) -+endif() -+ -+if(NOT smithwaterman_FOUND) -+ file(GLOB SW_INCLUDES contrib/smithwaterman/*.h*) -+ list(APPEND INCLUDES ${SW_INCLUDES}) -+endif() -+ - set(vcfwfa_SOURCE - src/legacy.cpp # introduces a WFA dependency - src/vcf-wfa.cpp -@@ -170,16 +188,24 @@ set(vcflib_SOURCE - src/LeftAlign.cpp - src/cigar.cpp - src/allele.cpp -- contrib/fastahack/Fasta.cpp -+ contrib/fsom/fsom.c -+ contrib/filevercmp/filevercmp.c -+ contrib/c-progress-bar/progress.c -+) -+ -+if(NOT fastahack_FOUND) -+ list(APPEND vcflib_SOURCE contrib/fastahack/Fasta.cpp) -+endif() -+ -+if(NOT smithwaterman_FOUND) -+ list(APPEND vcflib_SOURCE - contrib/smithwaterman/SmithWatermanGotoh.cpp - contrib/smithwaterman/Repeats.cpp - contrib/smithwaterman/IndelAllele.cpp - contrib/smithwaterman/disorder.cpp - contrib/smithwaterman/LeftAlign.cpp -- contrib/fsom/fsom.c -- contrib/filevercmp/filevercmp.c -- contrib/c-progress-bar/progress.c --) -+ ) -+endif() - - if (tabixpp_LOCAL) # add the tabixpp source file - list(APPEND vcflib_SOURCE ${tabixpp_SOURCE}) -@@ -440,6 +466,14 @@ if (NOT tabixpp_LOCAL) - target_link_libraries(vcflib PkgConfig::tabixpp) - endif() - -+if(fastahack_FOUND) -+ target_link_libraries(vcflib PkgConfig::fastahack) -+endif() -+ -+if(smithwaterman_FOUND) -+ target_link_libraries(vcflib PkgConfig::smithwaterman) -+endif() -+ - if(OPENMP) - target_link_libraries(vcflib OpenMP::OpenMP_CXX) - endif() diff --git a/manifest.scm.example b/manifest.scm.example index da257dc..a26c72a 100644 --- a/manifest.scm.example +++ b/manifest.scm.example @@ -34,4 +34,6 @@ "pggb" "seqwish" "smoothxg" + "pangenomes" + "mempang-workshop" )) diff --git a/opensmtpd-gn-fixes.patch b/opensmtpd-gn-fixes.patch new file mode 100644 index 0000000..e310bbe --- /dev/null +++ b/opensmtpd-gn-fixes.patch @@ -0,0 +1,48 @@ +diff -ruN opensmtpd-7.7.0p0.orig/usr.sbin/smtpd/smtpc.c opensmtpd-7.7.0p0/usr.sbin/smtpd/smtpc.c +--- opensmtpd-7.7.0p0.orig/usr.sbin/smtpd/smtpc.c 2026-04-17 10:19:15.152524476 +0000 ++++ opensmtpd-7.7.0p0/usr.sbin/smtpd/smtpc.c 2026-04-17 10:19:41.936756962 +0000 +@@ -114,8 +114,8 @@ + servname = value; + break; + case -1: +- if (suboptarg) +- fatalx("invalid TLS option \"%s\"", suboptarg); ++ //if (suboptarg) ++ // fatalx("invalid TLS option \"%s\"", suboptarg); + fatalx("missing TLS option"); + } + } +diff -ruN opensmtpd-7.7.0p0.orig/usr.sbin/smtpd/smtpctl.c opensmtpd-7.7.0p0/usr.sbin/smtpd/smtpctl.c +--- opensmtpd-7.7.0p0.orig/usr.sbin/smtpd/smtpctl.c 2026-04-17 10:19:15.156524511 +0000 ++++ opensmtpd-7.7.0p0/usr.sbin/smtpd/smtpctl.c 2026-04-17 10:19:15.212525001 +0000 +@@ -54,6 +54,8 @@ + #endif + #include <limits.h> + ++#include <grp.h> ++ + #include "smtpd.h" + #include "parser.h" + #include "log.h" +diff -ruN opensmtpd-7.7.0p0.orig/usr.sbin/smtpd/to.c opensmtpd-7.7.0p0/usr.sbin/smtpd/to.c +--- opensmtpd-7.7.0p0.orig/usr.sbin/smtpd/to.c 2026-04-17 10:19:15.156524511 +0000 ++++ opensmtpd-7.7.0p0/usr.sbin/smtpd/to.c 2026-04-17 10:19:15.252525351 +0000 +@@ -152,7 +152,7 @@ + time_to_text(time_t when) + { + struct tm *lt; +- static char buf[40]; ++ static char buf[50]; + const char *day[] = {"Sun", "Mon", "Tue", "Wed", "Thu", "Fri", "Sat"}; + const char *month[] = {"Jan","Feb","Mar","Apr","May","Jun", + "Jul","Aug","Sep","Oct","Nov","Dec"}; +@@ -169,6 +169,9 @@ + #elif defined HAVE_DECL_ALTZONE && defined HAVE_DECL_TIMEZONE + offset = lt->tm_isdst > 0 ? altzone : timezone; + tz = lt->tm_isdst > 0 ? tzname[1] : tzname[0]; ++#else ++ offset = 0; ++ tz = "GMT"; + #endif + + /* We do not use strftime because it is subject to locale substitution*/ diff --git a/gn/packages/patches/seqwish-paryfor-riscv.patch b/seqwish-paryfor-riscv.patch index cecf806..cecf806 100644 --- a/gn/packages/patches/seqwish-paryfor-riscv.patch +++ b/seqwish-paryfor-riscv.patch diff --git a/gn/packages/patches/seqwish-shared-library.patch b/seqwish-shared-library.patch index be982de..be982de 100644 --- a/gn/packages/patches/seqwish-shared-library.patch +++ b/seqwish-shared-library.patch |