diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 113 |
1 files changed, 67 insertions, 46 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 432589391b..3628d6231a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -295,9 +295,10 @@ BAM files.") (base32 "1vgw2mwngq20c530zim52zvgmw1lci8rzl33pvh44xqk3xlzvjsa")) (modules '((guix build utils))) - (snippet - ;; Delete bundled htslib. - '(delete-file-recursively "htslib-1.8")))) + (snippet '(begin + ;; Delete bundled htslib. + (delete-file-recursively "htslib-1.8") + #t)))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -1194,10 +1195,12 @@ errors at the end of reads.") "0hwa5r9qbglppb7sz5z79rlmmddr3n51n468jb3wh8rwjgn3yr90")) (modules '((guix build utils))) (snippet - '(substitute* "Makefile" - ;; replace BUILD_HOST and BUILD_TIME for deterministic build - (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"") - (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))))) + '(begin + (substitute* "Makefile" + ;; replace BUILD_HOST and BUILD_TIME for deterministic build + (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"") + (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")) + #t)))) (build-system gnu-build-system) (inputs `(("perl" ,perl) @@ -1391,10 +1394,12 @@ well as many of the command line options.") "15z2w3bvnc0n4qmb9bd6d8ylc2h2nj883x2w9iixf4x3vki9b22i")) (modules '((guix build utils))) (snippet - '(substitute* "setup.py" - ;; remove dependency on outdated "distribute" module - (("^from distribute_setup import use_setuptools") "") - (("^use_setuptools\\(\\)") ""))))) + '(begin + (substitute* "setup.py" + ;; remove dependency on outdated "distribute" module + (("^from distribute_setup import use_setuptools") "") + (("^use_setuptools\\(\\)") "")) + #t)))) (build-system python-build-system) (arguments `(#:tests? #f ;tests fail because test data are not included @@ -1426,9 +1431,11 @@ multiple sequence alignments.") (base32 "0dzap2axin9cbbl0d825w294bpn00zagfm1sigamm4v2pm5bj9lp")) (modules '((guix build utils))) - (snippet - ;; Drop bundled htslib. TODO: Also remove samtools and bcftools. - '(delete-file-recursively "htslib")))) + (snippet '(begin + ;; Drop bundled htslib. TODO: Also remove samtools + ;; and bcftools. + (delete-file-recursively "htslib") + #t)))) (build-system python-build-system) (arguments `(#:modules ((ice-9 ftw) @@ -1800,9 +1807,10 @@ time.") ;; for download from Sourceforge, but it has not been merged. (patches (search-patches "crossmap-allow-system-pysam.patch")) (modules '((guix build utils))) - ;; remove bundled copy of pysam - (snippet - '(delete-file-recursively "lib/pysam")))) + (snippet '(begin + ;; remove bundled copy of pysam + (delete-file-recursively "lib/pysam") + #t)))) (build-system python-build-system) (arguments `(#:python ,python-2 @@ -1911,7 +1919,8 @@ files.") (snippet '(begin ;; Delete bundled libBigWig sources - (delete-file-recursively "libBigWig"))))) + (delete-file-recursively "libBigWig") + #t)))) (build-system python-build-system) (arguments `(#:phases @@ -3145,6 +3154,8 @@ manipulating HTS data.") #:jdk ,icedtea-8 #:phases (modify-phases %standard-phases + ;; FIXME: this phase fails with "duplicate entry: htsjdk/samtools/AbstractBAMFileIndex$1.class" + (delete 'generate-jar-indices) (add-after 'unpack 'use-our-htsjdk (lambda* (#:key inputs #:allow-other-keys) (substitute* "build.xml" @@ -3202,6 +3213,8 @@ VCF.") (sxml xpath)) #:phases (modify-phases %standard-phases + ;; FIXME: this phase fails with "duplicate entry: htsjdk/samtools/AbstractBAMFileIndex$1.class" + (delete 'generate-jar-indices) (add-after 'unpack 'remove-useless-build.xml (lambda _ (delete-file "build.xml") #t)) ;; This is necessary to ensure that htsjdk is found when using @@ -3292,6 +3305,8 @@ VCF.") (list "-Dsamjdk.intel_deflater_so_path=lib/jni/libIntelDeflater.so") #:phases (modify-phases %standard-phases + ;; FIXME: This phase fails. + (delete 'generate-jar-indices) ;; Do not use bundled ant bzip2. (add-after 'unpack 'use-ant-bzip (lambda* (#:key inputs #:allow-other-keys) @@ -3870,9 +3885,11 @@ sequences).") "00fx14vpmgsijwxd1xql3if934l82v8ckqgjjyyhnr36qb9qrskv")) (modules '((guix build utils))) (snippet - ;; Delete bundled kseq. - ;; TODO: Also delete bundled murmurhash and open bloom filter. - '(delete-file "src/mash/kseq.h")))) + '(begin + ;; Delete bundled kseq. + ;; TODO: Also delete bundled murmurhash and open bloom filter. + (delete-file "src/mash/kseq.h") + #t)))) (build-system gnu-build-system) (arguments `(#:tests? #f ; No tests. @@ -4052,18 +4069,19 @@ assembled metagenomic sequence.") (base32 "1z3x0vd8ma7pdrnywj7i3kgwl89sdkwrrn62zl7r5calqaq2hyip")) (modules '((guix build utils))) - (snippet - '(substitute* "setup.py" - ;; Use setuptools, or else the executables are not - ;; installed. - (("distutils.core") "setuptools") - ;; use "gcc" instead of "cc" for compilation - (("^defines") - "cc.set_executables( + (snippet '(begin + (substitute* "setup.py" + ;; Use setuptools, or else the executables are not + ;; installed. + (("distutils.core") "setuptools") + ;; use "gcc" instead of "cc" for compilation + (("^defines") + "cc.set_executables( compiler='gcc', compiler_so='gcc', linker_exe='gcc', -linker_so='gcc -shared'); defines"))))) +linker_so='gcc -shared'); defines")) + #t)))) (build-system python-build-system) (arguments `(#:python ,python-2 ; only Python 2 is supported @@ -4864,7 +4882,8 @@ BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.") (("^from distribute_setup import use_setuptools") "") (("^use_setuptools\\(\\)") "") ;; do not use bundled copy of pysam - (("^have_pysam = False") "have_pysam = True")))))) + (("^have_pysam = False") "have_pysam = True")) + #t)))) (build-system python-build-system) (arguments `(#:python ,python-2)) (inputs @@ -4915,9 +4934,9 @@ distribution, coverage uniformity, strand specificity, etc.") "Data2DB" "PCL2Bin"))) (modify-phases %standard-phases - (add-before 'configure 'bootstrap + (replace 'bootstrap (lambda _ - (zero? (system* "bash" "gen_auto")))) + (invoke "bash" "gen_auto"))) (add-after 'build 'build-additional-tools (lambda* (#:key make-flags #:allow-other-keys) (every (lambda (dir) @@ -5420,9 +5439,10 @@ structures, classes for genomic regions, mapped sequencing reads, etc.") (sha256 (base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq")) (modules '((guix build utils))) - (snippet - ;; Remove bundled samtools. - '(delete-file-recursively "samtools")))) + (snippet '(begin + ;; Remove bundled samtools. + (delete-file-recursively "samtools") + #t)))) (build-system gnu-build-system) (arguments `(#:tests? #f ;no "check" target @@ -5627,10 +5647,11 @@ writing files into the .sra format.") (out (assoc-ref %outputs "out")) (doc (assoc-ref %outputs "doc"))) (setenv "PATH" (string-append tar "/bin:" bzip "/bin")) - (system* "tar" "xvf" (assoc-ref %build-inputs "source")) + (invoke "tar" "xvf" (assoc-ref %build-inputs "source")) (chdir (string-append "seqan-library-" ,version)) (copy-recursively "include" (string-append out "/include")) - (copy-recursively "share" (string-append doc "/share")))))) + (copy-recursively "share" (string-append doc "/share")) + #t)))) (native-inputs `(("source" ,source) ("tar" ,tar) @@ -11034,11 +11055,6 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (sha256 (base32 "0g38g8s3npr0gjm9fahlbhiskyfws9l5i0x1ml3rakzj7az5l9c9")))) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'bootstrap - (lambda _ (invoke "autoreconf" "-vif")))))) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) @@ -11952,7 +11968,8 @@ bytes of memory space, where n is the length of the string.") (snippet '(begin (delete-file-recursively "include/spdlog") (for-each delete-file '("include/xxhash.h" - "src/xxhash.c")))))) + "src/xxhash.c")) + #t)))) ("libdivsufsort" ,libdivsufsort) ("libgff" ,libgff) ("tbb" ,tbb) @@ -12677,7 +12694,8 @@ contains (snippet '(begin (for-each delete-file (find-files "jar/lib" "\\.jar$")) - (delete-file-recursively "3rdParty"))))) + (delete-file-recursively "3rdParty") + #t)))) (build-system ant-build-system) (arguments `(#:tests? #f ; test data are not included @@ -12696,6 +12714,9 @@ contains (guix build ant-build-system)) #:phases (modify-phases %standard-phases + ;; FIXME: fails with "java.io.FileNotFoundException: + ;; /gnu/store/q76y0ximcziplgfpbn26kbw4h3s14f33-dropseq-tools-1.13/share/java/lib/biojava-alignment.jar" + (delete 'generate-jar-indices) ;; All dependencies must be linked to "lib", because that's where ;; they will be searched for when the Class-Path property of the ;; manifest is computed. @@ -13053,7 +13074,7 @@ methylation and segmentation.") ("perl" ,perl) ("dropseq-tools" ,dropseq-tools) ("fastqc" ,fastqc) - ("java-picard" ,java-picard) + ("java-picard" ,java-picard-2.10.3) ; same as for dropseq ("java" ,icedtea-8) ("python-wrapper" ,python-wrapper) ("python-pyyaml" ,python-pyyaml) |