diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 99 |
1 files changed, 54 insertions, 45 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0aee5d180d..66504e9efd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -296,9 +296,10 @@ BAM files.") "0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz")) (patches (search-patches "bcftools-regidx-unsigned-char.patch")) (modules '((guix build utils))) - (snippet - ;; Delete bundled htslib. - '(delete-file-recursively "htslib-1.5")))) + (snippet '(begin + ;; Delete bundled htslib. + (delete-file-recursively "htslib-1.5") + #t)))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -1195,10 +1196,12 @@ 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) @@ -1392,10 +1395,12 @@ 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(modules '((guix build utils))) (snippet - '(substitute* "setup.py" - ;; remove dependency on outdated "distribute" module - (("^from distribute_setup import use_setuptools") "") - (("^use_setuptools\\(\\)") ""))))) + '(begin + (substitute* "setup.py" + ;; remove dependency on outdated "distribute" module + (("^from distribute_setup import use_setuptools") "") + (("^use_setuptools\\(\\)") "")) + #t)))) (build-system python-build-system)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 @@ -1427,9 +1432,11 @@ 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) @@ -1801,9 +1808,10 @@ 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 @@ -1912,7 +1920,8 @@ files.") (snippet '(begin ;; Delete bundled libBigWig sources - (delete-file-recursively "libBigWig"))))) + (delete-file-recursively "libBigWig") + #t)))) (build-system python-build-system) (arguments `(#:phases @@ -3786,9 +3795,11 @@ sequences).") "08znbvqq5xknfhmpp3wcj574zvi4p7i8zifi67c9qw9a6ikp42fj")) (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. @@ -3966,18 +3977,19 @@ 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 @@ -4778,7 +4790,8 @@ 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 @@ -4829,9 +4842,9 @@ 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) @@ -5334,9 +5347,10 @@ 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 @@ -10938,13 +10952,6 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (sha256 (base32 "0g38g8s3npr0gjm9fahlbhiskyfws9l5i0x1ml3rakzj7az5l9c9")))) - (arguments - (substitute-keyword-arguments (package-arguments htslib) - ((#:phases phases) - `(modify-phases ,phases - (add-after 'unpack 'bootstrap - (lambda _ - (zero? (system* "autoreconf" "-vif")))))))) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) @@ -11824,7 +11831,8 @@ 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) @@ -12549,7 +12557,8 @@ 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 |