[PATCH] gnu: Add f-seq.

DoneSubmitted by Ricardo Wurmus.
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3 participants
  • Ben Woodcroft
  • Ludovic Courtès
  • Ricardo Wurmus
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Ricardo Wurmus wrote on 15 Jun 2017 17:26
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(address . guix-patches@gnu.org)(name . Ricardo Wurmus)(address . ricardo.wurmus@mdc-berlin.de)
20170615152624.26092-1-ricardo.wurmus@mdc-berlin.de
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* gnu/packages/bioinformatics.scm (f-seq): New variable.--- gnu/packages/bioinformatics.scm | 50 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+)
Toggle diff (60 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex c1c0faf24..4c81f0741 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -9655,3 +9655,53 @@ browser.") (license (license:non-copyleft "http://genome.ucsc.edu/license/" "The contents of this package are free for all uses."))))++(define-public f-seq+ (let ((commit "6ccded34cff38cf432deed8503648b4a66953f9b")+ (revision "1"))+ (package+ (name "f-seq")+ (version (string-append "1.1-" revision "." commit))+ (source (origin+ (method git-fetch)+ (uri (git-reference+ (url "https://github.com/aboyle/F-seq.git")+ (commit commit)))+ (file-name (string-append name "-" version))+ (sha256+ (base32+ "1nk33k0yajg2id4g59bc4szr58r2q6pdq42vgcw054m8ip9wv26h"))+ (modules '((guix build utils)))+ ;; Remove bundled Java library archives.+ (snippet+ '(begin+ (for-each delete-file (find-files "lib" ".*"))+ #t))))+ (build-system ant-build-system)+ (arguments+ `(#:tests? #f ; no tests included+ #:phases+ (modify-phases %standard-phases+ (replace 'install+ (lambda* (#:key outputs #:allow-other-keys)+ (let* ((target (assoc-ref outputs "out"))+ (doc (string-append target "/share/doc/f-seq/")))+ (mkdir-p target)+ (mkdir-p doc)+ (substitute* "bin/linux/fseq"+ (("java") (which "java")))+ (install-file "README.txt" doc)+ (install-file "bin/linux/fseq" (string-append target "/bin"))+ (install-file "build~/fseq.jar" (string-append target "/lib"))+ (copy-recursively "lib" (string-append target "/lib"))+ #t))))))+ (inputs+ `(("perl" ,perl)+ ("java-commons-cli" ,java-commons-cli)))+ (home-page "http://fureylab.web.unc.edu/software/fseq/")+ (synopsis "Feature density estimator for high-throughput sequence tags")+ (description+ "F-Seq is a software package that generates a continuous tag sequence+density estimation allowing identification of biologically meaningful sites+whose output can be displayed directly in the UCSC Genome Browser.")+ (license license:gpl3+))))-- 2.13.0
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Ben Woodcroft wrote on 17 Jun 2017 05:31
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Hi Ricardo,

On 16/06/17 01:26, Ricardo Wurmus wrote:
Toggle quote (7 lines)> * gnu/packages/bioinformatics.scm (f-seq): New variable.> [..]> + (synopsis "Feature density estimator for high-throughput sequence tags")> + (description> + "F-Seq is a software package that generates a continuous tag sequence> +density estimation allowing identification of biologically meaningful sites> +whose output can be displayed directly in the UCSC Genome Browser.")
"features" is a little vague for me. How about something like this
"F-Seq is a software package that generates a continuous tag sequencedensity estimation allowing identification of biologically meaningful sites such as transcription factor binding sites (ChIP-seq) or regions of open chromatin (DNase-seq). Output can be displayed directly in the UCSC Genome Browser."

I also had some problems running this software in a container:
[env]# fseq/gnu/store/xjfxqh6rp4y4jwr4smwbvjqnikjbivai-profile/bin/fseq: line 30: sed: command not found/gnu/store/xjfxqh6rp4y4jwr4smwbvjqnikjbivai-profile/bin/fseq: line 32: sed: command not found/gnu/store/xjfxqh6rp4y4jwr4smwbvjqnikjbivai-profile/bin/fseq: line 30: sed: command not found/gnu/store/xjfxqh6rp4y4jwr4smwbvjqnikjbivai-profile/bin/fseq: line 32: sed: command not found/gnu/store/xjfxqh6rp4y4jwr4smwbvjqnikjbivai-profile/bin/fseq: line 62: dirname: command not foundError: Could not find or load main class edu.duke.igsp.gkde.Main
(exitstatus 1)

Given that the exitstatus of the above is non-zero, what about adding a cheap and cheerful test phase which simply runs "fseq -h" or similar?
Otherwise LGTM.
ben
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Ludovic Courtès wrote on 8 Sep 2017 17:51
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tags 27377 moreinfo
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Ricardo Wurmus wrote on 18 Oct 2017 23:54
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tags 27377 fixedclose 27377
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