aboutsummaryrefslogtreecommitdiff
path: root/gn
diff options
context:
space:
mode:
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/bioinformatics.scm229
-rw-r--r--gn/packages/genenetwork.scm18
-rw-r--r--gn/packages/ocaml.scm4
-rw-r--r--gn/packages/static.scm2
-rw-r--r--gn/services/databases.scm24
5 files changed, 151 insertions, 126 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index ed6d4d4..397b38f 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -1601,7 +1601,7 @@ runApp(launch.browser=0, port=4208)~%\n"
(define-public seqwish
(package
(name "seqwish")
- (version "0.7.9")
+ (version "0.7.11")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -1610,7 +1610,7 @@ runApp(launch.browser=0, port=4208)~%\n"
(recursive? #t)))
(file-name (git-file-name name version))
(sha256
- (base32 "0xnv40kjlb610bk67n4xdqz5dfsjhrqld5bxzblji57k6bb4n66x"))
+ (base32 "18wsrvqf0nsfk29v3ggdq2r4q15d4n4sq8v228qq1jsybbjlkgsa"))
(patches (search-patches "seqwish-paryfor-riscv.diff"
"seqwish-shared-library.diff"))
(snippet
@@ -1810,14 +1810,14 @@ dictionaries to record a queryable version of the graph.")
(define-public smoothxg
(package
(name "smoothxg")
- (version "0.7.2")
+ (version "0.8.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/pangenome/smoothxg"
"/releases/download/v" version
"/smoothxg-v" version ".tar.gz"))
(sha256
- (base32 "1px8b5aaa23z85i7ximdamk2jj7wk5hb7bpbrgxsvkxc69zlwy38"))
+ (base32 "1gl4dskj81hlma7wsjrwwg77hgzk7dc9iaqqnf2wzrf2f4ll1cdj"))
(snippet
#~(begin
(use-modules (guix build utils))
@@ -1855,7 +1855,8 @@ dictionaries to record a queryable version of the graph.")
(with-directory-excursion
(string-append "../smoothxg-v" #$version "/deps/abPOA")
(substitute* "Makefile"
- (("-march=native") ""))
+ (("-march=native") "")
+ (("-march=armv8-a\\+simd") ""))
(apply invoke "make" "libabpoa" make-flags)))))))
(inputs
(list jemalloc
@@ -1897,14 +1898,14 @@ The path-guided stochastic gradient descent based 1D sort implemented in
(define-public graphaligner
(package
(name "graphaligner")
- (version "1.0.14")
+ (version "1.0.19")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/maickrau/GraphAligner/files/"
- "7813545/GraphAligner.tar.gz"))
+ "14037134/GraphAligner.tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "1y4vwp03fl2ck6bnyn0sc97vgvdb8i0yfzjk5mv5gk0bc7a4f0n1"))))
+ (base32 "1z1rxvl2pmiqbh670phkx7vma36w90ylp27wyadlbzf32pa2cpdn"))))
(build-system gnu-build-system)
(arguments
(list
@@ -1938,17 +1939,18 @@ The path-guided stochastic gradient descent based 1D sort implemented in
(install-file header (string-append out "/include")))
(find-files "src" "\\.h(pp)?$"))))))))
(native-inputs
- `(("pkg-config" ,pkg-config)
- ("sparsehash" ,sparsehash)))
+ (list (list jemalloc "bin")
+ pkg-config
+ sparsehash))
(inputs
- `(("boost" ,boost)
- ("concurrentqueue" ,concurrentqueue)
- ("jemalloc" ,jemalloc)
- ("libdivsufsort" ,libdivsufsort)
- ("mummer" ,mummer)
- ("protobuf" ,protobuf)
- ("sdsl-lite" ,sdsl-lite)
- ("zlib" ,zlib)))
+ (list boost
+ concurrentqueue
+ jemalloc
+ libdivsufsort
+ mummer
+ protobuf
+ sdsl-lite
+ zlib))
(home-page "https://github.com/maickrau/GraphAligner")
(synopsis "Seed-and-extend program for aligning genome graphs")
(description "Seed-and-extend program for aligning long error-prone reads to
@@ -2141,7 +2143,7 @@ suitable for long reads, but works also well with short reads.")
(define-public odgi
(package
(name "odgi")
- (version "0.8.3")
+ (version "0.9.0")
(outputs '("out" "static"))
(source (origin
(method url-fetch)
@@ -2149,7 +2151,7 @@ suitable for long reads, but works also well with short reads.")
"/download/v" version
"/odgi-v" version ".tar.gz"))
(sha256
- (base32 "1gw1xdb945z25rar6pba6kq5xdx8l7fkhxjyrvc1z1brva53p9hk"))
+ (base32 "0brg0sz45v1wv4ld3p4jwiab10nyp2f691zfwpiva6g6f71q3cbk"))
(snippet
#~(begin
(use-modules (guix build utils))
@@ -3548,36 +3550,37 @@ protein alignments and syntenic genomic alignments.")
(define-public pplacer
(let ((commit "807f6f3"))
- (build-with-ocaml4.07
- (package
- (name "pplacer")
- ;; The commit should be updated with each version change.
- (version "1.1.alpha19")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/matsen/pplacer")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "11ppbbbx20p2g9wj3ff64dhnarb12q79v7qh4rk0gj6lkbz4n7cn"))))
- (build-system ocaml-build-system)
- (arguments
- `(#:modules ((guix build ocaml-build-system)
- (guix build utils)
- (ice-9 ftw))
+ (build-with-ocaml4.07
+ (package
+ (name "pplacer")
+ ;; The commit should be updated with each version change.
+ (version "1.1.alpha19")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/matsen/pplacer")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "11ppbbbx20p2g9wj3ff64dhnarb12q79v7qh4rk0gj6lkbz4n7cn"))))
+ (build-system ocaml-build-system)
+ (arguments
+ (list
+ #:modules '((guix build ocaml-build-system)
+ (guix build utils)
+ (ice-9 ftw))
#:phases
- (modify-phases %standard-phases
- (delete 'configure)
- (add-after 'unpack 'fix-build-with-latest-ocaml
- (lambda _
- (substitute* "myocamlbuild.ml"
- (("dep \\[\"c_pam\"\\]" m)
- (string-append "flag [\"ocaml\"; \"compile\"] (A \"-unsafe-string\");\n"
- m))
- (("let run_and_read" m)
- (string-append "
+ #~(modify-phases %standard-phases
+ (delete 'configure)
+ (add-after 'unpack 'fix-build-with-latest-ocaml
+ (lambda _
+ (substitute* "myocamlbuild.ml"
+ (("dep \\[\"c_pam\"\\]" m)
+ (string-append "flag [\"ocaml\"; \"compile\"] (A \"-unsafe-string\");\n"
+ m))
+ (("let run_and_read" m)
+ (string-append "
let split s ch =
let x = ref [] in
let rec go s =
@@ -3593,76 +3596,72 @@ let before_space s =
with Not_found -> s
" m))
- (("run_and_read \"ocamlfind list \\| cut -d' ' -f1\"" m)
- (string-append "List.map before_space (split_nl & " m ")"))
- ((" blank_sep_strings &") "")
- ((" Lexing.from_string &") ""))
- #t))
- (add-after 'unpack 'replace-bundled-cddlib
- (lambda* (#:key inputs #:allow-other-keys)
- (let* ((cddlib-src (assoc-ref inputs "cddlib-src"))
- (local-dir "cddlib_guix"))
- (mkdir local-dir)
- (with-directory-excursion local-dir
- (invoke "tar" "xvf" cddlib-src))
- (let ((cddlib-src-folder
- (string-append local-dir "/"
- (list-ref (scandir local-dir) 2)
- "/lib-src")))
- (for-each make-file-writable (find-files "cdd_src" ".*"))
- (for-each
- (lambda (file)
- (copy-file file
- (string-append "cdd_src/" (basename file))))
- (find-files cddlib-src-folder ".*[ch]$")))
- #t)))
- (add-after 'unpack 'fix-makefile
- (lambda _
- ;; Remove system calls to 'git'.
- (substitute* "Makefile"
- (("^DESCRIPT:=pplacer-.*")
- (string-append
- "DESCRIPT:=pplacer-$(shell uname)-v" ,version "\n")))
- (substitute* "myocamlbuild.ml"
- (("git describe --tags --long .*\\\" with")
- (string-append
- "echo -n v" ,version "-" ,commit "\" with")))
- #t))
- (replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (bin (string-append out "/bin")))
- (copy-recursively "bin" bin))
- #t)))
- #:ocaml ,ocaml-4.07
- #:findlib ,ocaml4.07-findlib))
- (inputs
- `(("zlib" ,zlib "static")
- ("gsl" ,gsl-static)
- ("ocaml-ounit" ,(package-with-ocaml4.07 ocaml-ounit))
- ("ocaml-batteries" ,(package-with-ocaml4.07 ocaml-batteries))
- ("ocaml-camlzip" ,(package-with-ocaml4.07 camlzip))
- ("ocaml-csv" ,(package-with-ocaml4.07 ocaml-csv))
- ("ocaml-sqlite3" ,(package-with-ocaml4.07 ocaml-sqlite3))
- ("ocaml-xmlm" ,(package-with-ocaml4.07 ocaml-xmlm))
- ("ocaml-mcl" ,(package-with-ocaml4.07 ocaml-mcl))
- ("ocaml-gsl" ,ocaml4.07-gsl-1)
- ("sqlite:static" ,sqlite "static")))
- (native-inputs
- `(("cddlib-src" ,(package-source cddlib))
- ("ocamlbuild" ,(package-with-ocaml4.07 ocamlbuild))
- ("pkg-config" ,pkg-config)))
- (propagated-inputs
- (list pplacer-scripts))
- (synopsis "Phylogenetic placement of biological sequences")
- (description
- "Pplacer places query sequences on a fixed reference phylogenetic tree
+ (("run_and_read \"ocamlfind list \\| cut -d' ' -f1\"" m)
+ (string-append "List.map before_space (split_nl & " m ")"))
+ ((" blank_sep_strings &") "")
+ ((" Lexing.from_string &") ""))))
+ (add-after 'unpack 'replace-bundled-cddlib
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let* ((cddlib-src (assoc-ref inputs "cddlib-src"))
+ (local-dir "cddlib_guix"))
+ (mkdir local-dir)
+ (with-directory-excursion local-dir
+ (invoke "tar" "xvf" cddlib-src))
+ (let ((cddlib-src-folder
+ (string-append local-dir "/"
+ (list-ref (scandir local-dir) 2)
+ "/lib-src")))
+ (for-each make-file-writable (find-files "cdd_src" ".*"))
+ (for-each
+ (lambda (file)
+ (copy-file file
+ (string-append "cdd_src/" (basename file))))
+ (find-files cddlib-src-folder ".*[ch]$"))))))
+ (add-after 'unpack 'fix-makefile
+ (lambda _
+ ;; Remove system calls to 'git'.
+ (substitute* "Makefile"
+ (("^DESCRIPT:=pplacer-.*")
+ (string-append
+ "DESCRIPT:=pplacer-$(shell uname)-v" ,version "\n")))
+ (substitute* "myocamlbuild.ml"
+ (("git describe --tags --long .*\\\" with")
+ (string-append
+ "echo -n v" ,version "-" ,commit "\" with")))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin")))
+ (copy-recursively "bin" bin)))))
+ #:ocaml ocaml-4.07
+ #:findlib ocaml4.07-findlib))
+ (inputs
+ (list (list zlib "static")
+ (list gsl "static")
+ (package-with-ocaml4.07 ocaml-ounit)
+ (package-with-ocaml4.07 ocaml-batteries)
+ (package-with-ocaml4.07 camlzip)
+ (package-with-ocaml4.07 ocaml-csv)
+ (package-with-ocaml4.07 ocaml-sqlite3)
+ (package-with-ocaml4.07 ocaml-xmlm)
+ (package-with-ocaml4.07 ocaml-mcl)
+ ocaml4.07-gsl-1
+ (list sqlite "static")))
+ (native-inputs
+ (list (package-source cddlib)
+ (package-with-ocaml4.07 ocamlbuild)
+ pkg-config))
+ (propagated-inputs
+ (list pplacer-scripts))
+ (synopsis "Phylogenetic placement of biological sequences")
+ (description
+ "Pplacer places query sequences on a fixed reference phylogenetic tree
to maximize phylogenetic likelihood or posterior probability according to a
reference alignment. Pplacer is designed to be fast, to give useful
information about uncertainty, and to offer advanced visualization and
downstream analysis.")
- (home-page "https://matsen.fhcrc.org/pplacer/")
- (license license:gpl3)))))
+ (home-page "https://matsen.fhcrc.org/pplacer/")
+ (license license:gpl3)))))
(define-public python2-biopython
(python2-package python-biopython))
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 8dad6d1..dbfd4e2 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -18,6 +18,7 @@
#:use-module (guix packages)
#:use-module (gnu packages)
#:use-module (gnu packages base)
+ #:use-module (gnu packages certs)
#:use-module (gnu packages bioconductor)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages check)
@@ -113,7 +114,7 @@
((#:tests? _ #f) #f)))))
(define-public genenetwork3
- (let ((commit "64c34e14de60f4c886587ebe35cfccfdcff2e0b4")
+ (let ((commit "0820295202c2fe747c05b93ce0f1c5a604442f69")
(revision "5"))
(package
(name "genenetwork3")
@@ -127,7 +128,7 @@
(file-name (git-file-name name version))
(sha256
(base32
- "1fhp74ggg2azk7s4nhyx44cwyvyr55az7w9n31np0ichpb30y3p9"))))
+ "1q4chw75ywrzgdhjh71c883dxzn71b92hsn4ipz7vj0bmymdcw53"))))
(inputs
(list python-click))
(native-inputs
@@ -138,6 +139,7 @@
(propagated-inputs
(list csvdiff
diffutils
+ nss-certs
gemma-wrapper
gn-rust-correlation
python-argon2-cffi
@@ -186,7 +188,7 @@
(license license:agpl3+))))
(define-public genenetwork2
- (let ((commit "2954770c642bc0da9b25aa55eb4c5182ccd0aad5")
+ (let ((commit "578a8ebe14bcc116c8cf12736a06cd56595b80fb")
(revision "4"))
(package
(name "genenetwork2")
@@ -199,12 +201,13 @@
(file-name (string-append name "-" version))
(sha256
(base32
- "1vj8fj6dfryqhbzhlm4nlv4cqx09pnws0lcis7ickk82ch93mkhf"))))
+ "059yhmq70j4wz5h66lmn68fijdb1j7236i7740dghrlminmak4a9"))))
(native-inputs
(list graphviz))
(propagated-inputs
(list genenetwork3
coreutils
+ nss-certs
gemma
gemma-wrapper
git
@@ -459,6 +462,7 @@
python-hypothesis))
(propagated-inputs
(list gunicorn
+ nss-certs
python-redis
python-flask
python-pyyaml
@@ -479,7 +483,7 @@
(license license:agpl3+))))
(define-public gn-auth
- (let ((commit "12edc160df0ead9ac1ae4e62a44d49582e063021")
+ (let ((commit "4c21d0e43cf0de1084d0e0a243e441c6e72236eb")
(revision "01"))
(package
(name "gn-auth")
@@ -493,7 +497,7 @@
(hash
(content-hash
(base32
- "11kixqv3rwfaad43bcqyh085gb0jfcpvzrlx66grkk73cqydgyzl")))))
+ "0z9qpgn0j9idzi975ykh04bq2r4pz5d0pppk2zvxiyhxxgxjydrx")))))
(build-system python-build-system)
(arguments
(list
@@ -512,6 +516,8 @@
python-pytest-mock))
(propagated-inputs
(list gunicorn
+ nss-certs
+ python-blinker
python-argon2-cffi
python-authlib
python-email-validator
diff --git a/gn/packages/ocaml.scm b/gn/packages/ocaml.scm
index 7c6020a..cb97868 100644
--- a/gn/packages/ocaml.scm
+++ b/gn/packages/ocaml.scm
@@ -40,9 +40,9 @@
"0nzp43hp8pbjqkrxnwp5lgjrabxayf61h18fjaydi0s5faq6f3xh"))))
(build-system ocaml-build-system)
(inputs
- `(("gsl" ,gsl-static)))
+ (list (list gsl "static")))
(native-inputs
- `(("ocamlbuild" ,ocamlbuild)))
+ (list ocamlbuild))
(arguments '())
(propagated-inputs '()))))
diff --git a/gn/packages/static.scm b/gn/packages/static.scm
index 8b43cdb..67b4873 100644
--- a/gn/packages/static.scm
+++ b/gn/packages/static.scm
@@ -64,7 +64,7 @@
(string-append all " atomic pthread")))))))))
(inputs
(list atomic-queue
- gsl-static
+ (list gsl "static")
htslib-minimal
jemalloc
(list zlib "static")
diff --git a/gn/services/databases.scm b/gn/services/databases.scm
index 937aa9e..91ac166 100644
--- a/gn/services/databases.scm
+++ b/gn/services/databases.scm
@@ -42,7 +42,20 @@
(http-server-ip virtuoso-configuration-http-server-ip
(default "localhost"))
(http-server-port virtuoso-configuration-http-server-port
- (default 8890)))
+ (default 8890))
+ (checkpoint-interval virtuoso-configuration-checkpoint-interval
+ (default "60"))
+ (scheduler-interval virtuoso-configuration-scheduler-interval
+ (default "10"))
+ ;; Database settings
+ (database-file virtuoso-configuration-database-file
+ (default "/var/lib/virtuoso/virtuoso.db"))
+ (lock-file virtuoso-configuration-lock-file
+ (default "/var/lib/virtuoso/virtuoso.lck"))
+ (transaction-file virtuoso-configuration-transaction-file
+ (default "/var/lib/virtuoso/virtuoso.trx"))
+ (syslog virtuoso-configuration-syslog
+ (default "0")))
(define (virtuoso-activation config)
(with-imported-modules '((guix build utils))
@@ -67,6 +80,7 @@
(home-directory "/var/lib/virtuoso")
(shell (file-append shadow "/sbin/nologin")))))
+
(define (virtuoso-shepherd-service config)
(shepherd-service
(documentation "Run Virtuoso.")
@@ -100,7 +114,13 @@
(format port "[HTTPServer]~%")
(format port "ServerPort = ~a:~a~%"
#$(virtuoso-configuration-http-server-ip config)
- #$(virtuoso-configuration-http-server-port config)))))))
+ #$(virtuoso-configuration-http-server-port config)))
+ (format port
+ "[Database]~%DatabaseFile = ~a~%LockFile = ~a~%TransactionFile = ~a~%Syslog = ~a~%"
+ #$(virtuoso-configuration-database-file config)
+ #$(virtuoso-configuration-lock-file config)
+ #$(virtuoso-configuration-transaction-file config)
+ #$(virtuoso-configuration-syslog config))))))
#:directory #$(virtuoso-configuration-state-directory config)
#:user "virtuoso"
#:group "virtuoso"
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-09 19:19:09 +0000