Package: guix-patches;
Reported by: Maxime Devos <maximedevos <at> telenet.be>
Date: Fri, 2 Jul 2021 10:05:01 UTC
Severity: normal
Tags: patch
Done: Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
Bug is archived. No further changes may be made.
View this message in rfc822 format
From: Maxime Devos <maximedevos <at> telenet.be> To: 49327 <at> debbugs.gnu.org Cc: Maxime Devos <maximedevos <at> telenet.be> Subject: [bug#49327] [PATCH core-updates 008/128] gnu: bioinformatics: Add 'bash' input for 'wrap-program'. Date: Fri, 2 Jul 2021 12:06:14 +0200
It is required for cross-compilation.
* gnu/packages/bioinformatics.scm
(bamm)[inputs]: Add 'bash-minimal'.
(ribotaper)[inputs]: Likewise.
(bioperl-minimal)[inputs]: Likewise.
(tetoolkit)[inputs]: Likewise.
(couger)[inputs]: Likewise.
(repeat-masker)[inputs]: Likewise.
(edirect)[inputs]: Likewise.
(mafft)[inputs]: Likewise.
(prank)[inputs]: Likewise.
(roary)[inputs]: Likewise.
(rsem)[inputs]: Likewise.
(shorah)[inputs]: Likewise.
(rcas-web)[inputs]: Likewise.
(filtlong)[inputs]: Likewise.
(nanopolish)[inputs]: Likewise.
(find-circ)[inputs]: Likewise.
(arriba)[inputs]: Likewise.
(pplacer-scripts)[inputs]: Likewise.
(ensembl-vep)[inputs]: Likewise.
---
gnu/packages/bioinformatics.scm | 54 ++++++++++++++++++++++-----------
1 file changed, 37 insertions(+), 17 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 64fc6173db..6af530298c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -263,6 +263,7 @@ structure of the predicted RNA.")
(inputs
`(("htslib" ,htslib-1.3) ; At least one test fails on htslib-1.4+.
("samtools" ,samtools)
+ ("bash" ,bash-minimal) ; for wrap-program
("bwa" ,bwa)
("grep" ,grep)
("sed" ,sed)
@@ -757,7 +758,8 @@ cpp.find_library('hdf5_cpp', dirs : '~a'), "
"Ribotaper.sh")))
#t)))))
(inputs
- `(("bedtools" ,bedtools-2.18)
+ `(("bash" ,bash-minimal) ; for wrap-program
+ ("bedtools" ,bedtools-2.18)
("samtools" ,samtools-0.1)
("r-minimal" ,r-minimal)
("r-foreach" ,r-foreach)
@@ -1166,7 +1168,9 @@ alignments and perform the following operations:
`("PERL5LIB" ":" prefix (,path))))
(find-files bin "\\.pl$"))
#t))))))
- (inputs inputs)
+ (inputs
+ `(("bash" ,bash-minimal) ; for wrap-program
+ ,@inputs))
(native-inputs
`(("perl-test-most" ,perl-test-most)))
(home-page "https://metacpan.org/release/BioPerl")
@@ -2226,6 +2230,7 @@ high-throughput sequencing data – with an emphasis on simplicity.")
#t)))))
(inputs
`(("coreutils" ,coreutils)
+ ("bash" ,bash-minimal) ; for wrap-program
("bedtools" ,bedtools)
("python-argparse" ,python2-argparse)
("python-pysam" ,python2-pysam)
@@ -2423,7 +2428,8 @@ gene predictor designed to work with assembled, aligned RNA-seq transcripts.")
`("GUIX_PYTHONPATH" ":" prefix (,path))))
#t)))))
(inputs
- `(("python" ,python-2)
+ `(("bash" ,bash-minimal) ; for wrap-program
+ ("python" ,python-2)
("python2-pillow" ,python2-pillow)
("python2-numpy" ,python2-numpy)
("python2-scipy" ,python2-scipy)
@@ -3001,7 +3007,8 @@ bases are detected.")
(wrap-program (string-append bin "/RepeatMasker")
`("PERL5LIB" ":" prefix (,path ,share)))))))))
(inputs
- `(("perl" ,perl)
+ `(("bash" ,bash-minimal) ; for wrap-program
+ ("perl" ,perl)
("perl-text-soundex" ,perl-text-soundex)
("python" ,python)
("python-h5py" ,python-h5py)
@@ -3255,7 +3262,8 @@ quantitative phenotypes.")
"-filter" "-help")
#t)))))
(inputs
- `(("edirect-go-programs" ,edirect-go-programs)
+ `(("bash" ,bash-minimal) ; for wrap-program
+ ("edirect-go-programs" ,edirect-go-programs)
("perl-html-parser" ,perl-html-parser)
("perl-encode-locale" ,perl-encode-locale)
("perl-file-listing" ,perl-file-listing)
@@ -4952,7 +4960,8 @@ sequencing tag position and orientation.")
(find-files bin)))
#t)))))
(inputs
- `(("perl" ,perl)
+ `(("bash" ,bash-minimal) ; for wrap-program
+ ("perl" ,perl)
("ruby" ,ruby)
("gawk" ,gawk)
("grep" ,grep)
@@ -5485,7 +5494,8 @@ generated using the PacBio Iso-Seq protocol.")
(install-file "prank.1" man))
#t)))))
(inputs
- `(("mafft" ,mafft)
+ `(("bash" ,bash-minimal) ; for wrap-program
+ ("mafft" ,mafft)
("exonerate" ,exonerate)
("bppsuite" ,bppsuite)))
(home-page "http://wasabiapp.org/software/prank/")
@@ -5718,7 +5728,8 @@ partial genes, and identifies translation initiation sites.")
("perl-test-most" ,perl-test-most)
("perl-test-output" ,perl-test-output)))
(inputs
- `(("perl-array-utils" ,perl-array-utils)
+ `(("bash" ,bash-minimal) ; for wrap-program
+ ("perl-array-utils" ,perl-array-utils)
("bioperl" ,bioperl-minimal)
("perl-digest-md5-file" ,perl-digest-md5-file)
("perl-exception-class" ,perl-exception-class)
@@ -5871,7 +5882,8 @@ phylogenies.")
"rsem-run-prsem-testing-procedure")))
#t)))))
(inputs
- `(("boost" ,boost)
+ `(("bash" ,bash-minimal) ; for wrap-program
+ ("boost" ,boost)
("r-minimal" ,r-minimal)
("perl" ,perl)
("htslib" ,htslib-1.3)
@@ -7764,7 +7776,8 @@ data. It also generates basic statistics for your sequences.")
(when tests?
(invoke "make" "check")))))))
(inputs
- `(("boost" ,boost)
+ `(("bash" ,bash-minimal) ; for wrap-program
+ ("boost" ,boost)
("htslib" ,htslib)
("python" ,python)
("python-biopython" ,python-biopython)
@@ -8035,7 +8048,8 @@ secondary structure and comparative analysis in R.")
`("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
#t)))))
(inputs
- `(("r-minimal" ,r-minimal)
+ `(("bash" ,bash-minimal) ; for wrap-program
+ ("r-minimal" ,r-minimal)
("r-rcas" ,r-rcas)
("guile" ,guile-2.2)
("guile-json" ,guile-json-1)
@@ -11189,7 +11203,8 @@ conversions, region filtering, FASTA sequence extraction and more.")
"unmapped2anchors.py")))
#t)))))
(inputs
- `(("python2" ,python-2)
+ `(("bash" ,bash-minimal) ; for wrap-program
+ ("python2" ,python-2)
("python2-pysam" ,python2-pysam)
("python2-numpy" ,python2-numpy)))
(home-page "https://github.com/marvin-jens/find_circ")
@@ -12329,7 +12344,8 @@ datasets.")
(("awk") (which "gawk")))
#t)))))
(inputs
- `(("gawk" ,gawk) ;for read_info_histograms.sh
+ `(("bash" ,bash-minimal) ;for wrap-program
+ ("gawk" ,gawk) ;for read_info_histograms.sh
("python" ,python-2) ;required for histogram.py
("zlib" ,zlib)))
(home-page "https://github.com/rrwick/Filtlong/")
@@ -12407,7 +12423,8 @@ choosing which reads pass the filter.")
`("PERL5LIB" ":" prefix (,perl5lib))))
(find-files scripts "\\.pl"))))))))
(inputs
- `(("guile" ,guile-3.0) ; for wrappers
+ `(("bash" ,bash-minimal) ; for wrap-program
+ ("guile" ,guile-3.0) ; for other wrappers
("eigen" ,eigen)
("hdf5" ,hdf5)
("htslib" ,htslib)
@@ -12707,7 +12724,8 @@ includes a command line tool and an analysis pipeline.")
`("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE")))))
#t)))))
(inputs
- `(("htslib" ,htslib)
+ `(("bash" ,bash-minimal) ; for wrap-program
+ ("htslib" ,htslib)
("r-minimal" ,r-minimal)
("r-circlize" ,r-circlize)
("r-genomicalignments" ,r-genomicalignments)
@@ -12914,7 +12932,8 @@ downstream analysis.")
`("PATH" ":" prefix (,path)))))
#t)))))
(inputs
- `(("infernal" ,infernal)
+ `(("bash" ,bash-minimal) ; for wrap-program
+ ("infernal" ,infernal)
("hmmer" ,hmmer)))
(propagated-inputs
`(("python-biopython" ,python2-biopython)
@@ -14172,7 +14191,8 @@ my @test_files = map {\"$dirname\\/t\\/\".$_} grep {!/^\\./ && /\\.t$/} readdir
runtests(@test_files);
"))))))))
(inputs
- `(("bioperl-minimal" ,bioperl-minimal)
+ `(("bash" ,bash-minimal) ; for wrap-program
+ ("bioperl-minimal" ,bioperl-minimal)
("perl-bio-db-hts" ,perl-bio-db-hts)
("perl-dbi" ,perl-dbi)
("perl-dbd-mysql" ,perl-dbd-mysql)
--
2.32.0
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Copyright (C) 1999 Darren O. Benham,
1997,2003 nCipher Corporation Ltd,
1994-97 Ian Jackson.