From 2ac3b2d76b8378803cb9dac9949ca3e5f6086157 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Wed, 8 Apr 2026 17:54:57 +0000 Subject: Rename channels.scm to avoid guix pull compilation error [AI] Rename manifest.scm to avoid guix pull compilation error [AI] Replace local-file with git-fetch statements --- README.org | 4 ++-- channels.scm | 5 ----- channels.scm.example | 5 +++++ gn/packages/genenetwork-rust.scm | 33 ++++++++++++++++++++++----------- gn/packages/pangenome-rust.scm | 26 ++++++++++++++++++++------ manifest.scm | 37 ------------------------------------- manifest.scm.example | 37 +++++++++++++++++++++++++++++++++++++ 7 files changed, 86 insertions(+), 61 deletions(-) delete mode 100644 channels.scm create mode 100644 channels.scm.example delete mode 100644 manifest.scm create mode 100644 manifest.scm.example diff --git a/README.org b/README.org index 6e63108..5d7cc33 100644 --- a/README.org +++ b/README.org @@ -71,9 +71,9 @@ root with * Testing the build -All important packages are listed in manifest.scm. Test with +All important packages are listed in manifest.scm.example. Test with -: guix build -L . -m manifest.scm +: guix build -L . -m manifest.scm.example * An important note on AI diff --git a/channels.scm b/channels.scm deleted file mode 100644 index f7d1930..0000000 --- a/channels.scm +++ /dev/null @@ -1,5 +0,0 @@ -;; example channels.scm -(list (channel - (name 'guix-bioinformatics) - (url "https://git.genenetwork.org/guix-bioinformatics") - (branch "main"))) diff --git a/channels.scm.example b/channels.scm.example new file mode 100644 index 0000000..f7d1930 --- /dev/null +++ b/channels.scm.example @@ -0,0 +1,5 @@ +;; example channels.scm +(list (channel + (name 'guix-bioinformatics) + (url "https://git.genenetwork.org/guix-bioinformatics") + (branch "main"))) diff --git a/gn/packages/genenetwork-rust.scm b/gn/packages/genenetwork-rust.scm index 54b8389..78e9130 100644 --- a/gn/packages/genenetwork-rust.scm +++ b/gn/packages/genenetwork-rust.scm @@ -555,13 +555,19 @@ ) (define-public rust-qtlreaper + (let ((commit "4dafa7289432d10685b6b235e3552ac3d681bb03") + (revision "0")) (package (name "rust-qtlreaper") - (version "0.1.4") - ;; Use local source with updated Cargo.lock for modern Rust. - ;; Push Cargo.lock upstream, then switch to git-fetch. - (source (local-file "/fast/pjotr/tmp/claude/factory/rust-qtlreaper" - #:recursive? #t)) + (version (git-version "0.1.4" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/genenetwork/rust-qtlreaper") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1p7dmxh43ly0k7q6va0lzisqnk1i7af3dy5aw1sr4y5s7z0h6i0y")))) (build-system cargo-build-system) (arguments (list #:install-source? #f #:tests? #f)) ; test results vary by machine @@ -572,17 +578,22 @@ (description "Rust-qtlreaper is a Rust implementation of QTL Reaper for mapping quantitative trait loci (QTL) in genetic datasets.") - (license license:agpl3+))) + (license license:agpl3+)))) (define-public gn-rust-correlation - (let ((commit "48604d86471df965f189e46580578b24191add0e") - (revision "0")) + (let ((commit "473ad82b6f4477bbbeeef977e3e9f830f59a9b7f") + (revision "1")) (package (name "gn-rust-correlation") (version (git-version "0.1.4" revision commit)) - ;; Use local source with updated Cargo.lock for modern Rust. - (source (local-file "/fast/pjotr/tmp/claude/factory/correlation_rust" - #:recursive? #t)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Alexanderlacuna/correlation_rust") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1xlasa4ggyynmnm890i7zlsqds7jfclmh5s6p582xlfdf75k9h5z")))) (build-system cargo-build-system) (native-inputs (list gsl)) (arguments (list #:install-source? #f)) diff --git a/gn/packages/pangenome-rust.scm b/gn/packages/pangenome-rust.scm index 913f7f3..7bd2d6b 100644 --- a/gn/packages/pangenome-rust.scm +++ b/gn/packages/pangenome-rust.scm @@ -3848,8 +3848,14 @@ collapses them into a non-redundant graph structure.") (package (name "gafpack") (version (git-version "0.0.0" revision commit)) - (source (local-file "/fast/pjotr/tmp/claude/factory/gafpack" - #:recursive? #t)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/gafpack") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0di2psh0ls7jlbnqs7k71p55f73pn23a09k1h3ril7gwjcrzr3rk")))) (build-system cargo-build-system) (arguments (list #:install-source? #f)) (inputs (cargo-inputs 'gafpack #:module '(gn packages pangenome-rust))) @@ -3861,11 +3867,19 @@ maps useful in haplotype-based genotyping.") (license license:expat)))) (define-public vcfbub + (let ((commit "26a1f0cb216a423f8547c4ad0e0ce38cb9d324b9") + (revision "0")) (package (name "vcfbub") - (version "0.1.0") - (source (local-file "/fast/pjotr/tmp/claude/factory/vcfbub" - #:recursive? #t)) + (version (git-version "0.1.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pangenome/vcfbub") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1j91b4mba0gpghix0sn6m6a81722vzhpf5a2b03ysrqsrvfykk5z")))) (build-system cargo-build-system) (arguments (list #:install-source? #f)) (inputs (cargo-inputs 'vcfbub #:module '(gn packages pangenome-rust))) @@ -3873,4 +3887,4 @@ maps useful in haplotype-based genotyping.") (synopsis "Popping bubbles in vg deconstruct VCFs") (description "vcfbub filters VCF records by snarl tree level and allele size, keeping nested bubbles when parent bubbles are popped.") - (license license:expat))) + (license license:expat)))) diff --git a/manifest.scm b/manifest.scm deleted file mode 100644 index da257dc..0000000 --- a/manifest.scm +++ /dev/null @@ -1,37 +0,0 @@ -;; Guix manifest for all end-node packages in guix-bioinformatics. -;; These are packages not depended on by other packages in this channel. -;; -;; Usage: -;; guix build -L guix-bioinformatics -m manifest.scm -;; - -(specifications->manifest - '( - "bnw" - "bwa-mem2" - "cosigt" - "gafpack" - "gemma-wrapper" - "genecup" - "genenetwork2" - "genenetwork3" - "gfainject" - "gfautil" - "gn-auth" - "gn-guile" - "gn-libs" - "gn-proxy" - "gn-uploader" - "impg" - "julia-pluto" - "logtodo" - "mbg" - "meryl" - "miniprot" - "moosefs" - "odgi" - "pangene" - "pggb" - "seqwish" - "smoothxg" - )) diff --git a/manifest.scm.example b/manifest.scm.example new file mode 100644 index 0000000..da257dc --- /dev/null +++ b/manifest.scm.example @@ -0,0 +1,37 @@ +;; Guix manifest for all end-node packages in guix-bioinformatics. +;; These are packages not depended on by other packages in this channel. +;; +;; Usage: +;; guix build -L guix-bioinformatics -m manifest.scm +;; + +(specifications->manifest + '( + "bnw" + "bwa-mem2" + "cosigt" + "gafpack" + "gemma-wrapper" + "genecup" + "genenetwork2" + "genenetwork3" + "gfainject" + "gfautil" + "gn-auth" + "gn-guile" + "gn-libs" + "gn-proxy" + "gn-uploader" + "impg" + "julia-pluto" + "logtodo" + "mbg" + "meryl" + "miniprot" + "moosefs" + "odgi" + "pangene" + "pggb" + "seqwish" + "smoothxg" + )) -- cgit 1.4.1