diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 60 |
1 files changed, 38 insertions, 22 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 782af294e0..026527cd36 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -281,7 +281,8 @@ instance, it implements several methods to assess contig-wise read coverage.") (setenv "LDFLAGS" (string-append "-Wl,-rpath=" - (assoc-ref outputs "out") "/lib/bamtools"))))))) + (assoc-ref outputs "out") "/lib/bamtools")) + #t))))) (inputs `(("zlib" ,zlib))) (home-page "https://github.com/pezmaster31/bamtools") (synopsis "C++ API and command-line toolkit for working with BAM data") @@ -496,7 +497,8 @@ BED, GFF/GTF, VCF.") '("create_annotations_files.bash" "create_metaplots.bash" "Ribotaper_ORF_find.sh" - "Ribotaper.sh")))))))) + "Ribotaper.sh"))) + #t))))) (inputs `(("bedtools" ,bedtools-2.18) ("samtools" ,samtools-0.1) @@ -591,7 +593,8 @@ independently with transcriptional regulation.") (man (string-append out "/share/man/man1"))) (mkdir-p man) (copy-file "awk.1" (string-append man "/bioawk.1")) - (install-file "bioawk" bin))))))) + (install-file "bioawk" bin)) + #t))))) (home-page "https://github.com/lh3/bioawk") (synopsis "AWK with bioinformatics extensions") (description "Bioawk is an extension to Brian Kernighan's awk, adding the @@ -1240,7 +1243,7 @@ confidence to have in an alignment.") '(#:tests? #f ;no "check" target #:make-flags (list (string-append "ZLIB=" - (assoc-ref %build-inputs "zlib") + (assoc-ref %build-inputs "zlib:static") "/lib/libz.a") (string-append "LDFLAGS=" (string-join '("-lboost_filesystem" @@ -1283,6 +1286,7 @@ confidence to have in an alignment.") ("boost" ,boost) ("sparsehash" ,sparsehash) ("pigz" ,pigz) + ("zlib:static" ,zlib "static") ("zlib" ,zlib))) (supported-systems '("x86_64-linux")) (home-page "https://sourceforge.net/p/bless-ec/wiki/Home/") @@ -1811,7 +1815,8 @@ databases.") (copy-recursively "QuarryFiles" (string-append out "/QuarryFiles")) (install-file "CodingQuarry" bin) - (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin))))))) + (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin)) + #t))))) (inputs `(("openmpi" ,openmpi))) (native-search-paths (list (search-path-specification @@ -2727,7 +2732,8 @@ Illumina, Roche 454, and the SOLiD platform.") (share (string-append out "/share/fraggenescan/train"))) (install-file "run_FragGeneScan.pl" bin) (install-file "FragGeneScan" bin) - (copy-recursively "train" share)))) + (copy-recursively "train" share)) + #t)) (delete 'check) (add-after 'install 'post-install-check ;; In lieu of 'make check', run one of the examples and check the @@ -4153,7 +4159,8 @@ probabilistic distances of genome abundance and tetranucleotide frequency.") "#!" (assoc-ref inputs "bash") "/bin/sh\n\n" (assoc-ref inputs "jre") "/bin/java -jar " bin "/minced.jar \"$@\"\n")))) - (chmod wrapper #o555))))))) + (chmod wrapper #o555)) + #t))))) (native-inputs `(("jdk" ,icedtea "jdk"))) (inputs @@ -4408,7 +4415,7 @@ downstream analysis.") #:phases (modify-phases %standard-phases (add-after 'unpack 'enter-scripts-dir - (lambda _ (chdir "scripts"))) + (lambda _ (chdir "scripts") #t)) (replace 'check (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t)) (add-after 'install 'wrap-executables @@ -5222,6 +5229,7 @@ viewer.") #t)))))) (inputs `(("perl" ,perl) + ("zlib:static" ,zlib "static") ("zlib" ,zlib))) (supported-systems '("x86_64-linux")) (home-page "https://github.com/wanpinglee/MOSAIK") @@ -6019,7 +6027,8 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.") (lambda _ (substitute* "Makefile" (("(COMPILATION_TIME_PLACE=\")(.*)(\")" _ pre mid post) - (string-append pre "Built with Guix" post))))) + (string-append pre "Built with Guix" post))) + #t)) (add-after 'enter-source-dir 'do-not-use-bundled-htslib (lambda _ (substitute* "Makefile" @@ -6103,7 +6112,8 @@ sequences.") (lambda* (#:key outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) (mkdir-p bin) - (copy-recursively "../bin" bin)))) + (copy-recursively "../bin" bin)) + #t)) ;; no "configure" script (delete 'configure)))) (inputs `(("zlib" ,zlib))) @@ -12007,11 +12017,13 @@ bytes of memory space, where n is the length of the string.") (add-after 'unpack 'do-not-look-for-boost (lambda* (#:key inputs #:allow-other-keys) (substitute* "CMakeLists.txt" - (("find_package\\(Boost 1\\.53\\.0") "#")))) + (("find_package\\(Boost 1\\.53\\.0") "#")) + #t)) (add-after 'unpack 'do-not-assign-to-macro (lambda _ (substitute* "include/spdlog/details/format.cc" - (("const unsigned CHAR_WIDTH = 1;") "")))) + (("const unsigned CHAR_WIDTH = 1;") "")) + #t)) (add-after 'unpack 'prepare-rapmap (lambda* (#:key inputs #:allow-other-keys) (let ((src "external/install/src/rapmap/") @@ -12027,7 +12039,8 @@ bytes of memory space, where n is the length of the string.") (for-each (lambda (file) (install-file file src)) (find-files "/tmp/rapmap/src" "\\.(c|cpp)")) - (copy-recursively "/tmp/rapmap/include" include)))) + (copy-recursively "/tmp/rapmap/include" include)) + #t)) (add-after 'unpack 'use-system-libraries (lambda* (#:key inputs #:allow-other-keys) (substitute* '("src/SailfishIndexer.cpp" @@ -12067,7 +12080,8 @@ bytes of memory space, where n is the length of the string.") (string-append (getenv "CPLUS_INCLUDE_PATH") ":" (assoc-ref inputs "eigen") - "/include/eigen3"))))))) + "/include/eigen3")) + #t))))) (inputs `(("boost" ,boost) ("eigen" ,eigen) @@ -12253,11 +12267,13 @@ performance as its primary goal.") (add-after 'unpack 'do-not-look-for-boost (lambda* (#:key inputs #:allow-other-keys) (substitute* "CMakeLists.txt" - (("find_package\\(Boost 1\\.53\\.0") "#")))) + (("find_package\\(Boost 1\\.53\\.0") "#")) + #t)) (add-after 'unpack 'do-not-phone-home (lambda _ (substitute* "src/Salmon.cpp" - (("getVersionMessage\\(\\)") "\"\"")))) + (("getVersionMessage\\(\\)") "\"\"")) + #t)) (add-after 'unpack 'prepare-rapmap (lambda* (#:key inputs #:allow-other-keys) (let ((src "external/install/src/rapmap/") @@ -12274,7 +12290,8 @@ performance as its primary goal.") "external/install/include/rapmap/concurrentqueue.h" "external/install/include/rapmap/FastxParserThreadUtils.hpp" "external/install/src/rapmap/FastxParser.cpp" - "external/install/src/rapmap/xxhash.c"))))) + "external/install/src/rapmap/xxhash.c"))) + #t)) (add-after 'unpack 'use-system-libraries (lambda* (#:key inputs #:allow-other-keys) (substitute* "src/CMakeLists.txt" @@ -12385,8 +12402,7 @@ variational inference.") (propagated-inputs `(("python-h5py" ,python-h5py) ("python-numpy" ,python-numpy) - ("python-scipy" ,python-scipy) - ("python-typing" ,python-typing))) + ("python-scipy" ,python-scipy))) (home-page "https://github.com/linnarsson-lab/loompy") (synopsis "Work with .loom files for single-cell RNA-seq data") (description "The loom file format is an efficient format for very large @@ -13059,7 +13075,7 @@ expression report comparing samples in an easily configurable manner.") ("fastqc" ,fastqc) ("bowtie" ,bowtie) ("idr" ,idr) - ("snakemake" ,snakemake-4) + ("snakemake" ,snakemake) ("samtools" ,samtools) ("bedtools" ,bedtools) ("kentutils" ,kentutils))) @@ -13120,7 +13136,7 @@ in an easily configurable manner.") ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) ("python-wrapper" ,python-wrapper) ("python-pyyaml" ,python-pyyaml) - ("snakemake" ,snakemake-4) + ("snakemake" ,snakemake) ("bismark" ,bismark) ("fastqc" ,fastqc) ("bowtie" ,bowtie) @@ -13170,7 +13186,7 @@ methylation and segmentation.") ("ghc-pandoc" ,ghc-pandoc) ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) ("samtools" ,samtools) - ("snakemake" ,snakemake-4) + ("snakemake" ,snakemake) ("star" ,star) ("r-minimal" ,r-minimal) ("r-argparser" ,r-argparser) |