From: ludo@gnu.org (Ludovic Courtès)
To: pimi <madalinionel.patrascu@mdc-berlin.de>
Cc: ricardo.wurmus@mdc-berlin.de, 32984-done@debbugs.gnu.org
Subject: bug#32984: [PATCH] gnu: Add filtlong.
Date: Mon, 08 Oct 2018 18:32:06 +0200 [thread overview]
Message-ID: <87murowgah.fsf@gnu.org> (raw)
In-Reply-To: <20181008091741.31531-1-madalinionel.patrascu@mdc-berlin.de> (pimi's message of "Mon, 8 Oct 2018 11:17:41 +0200")
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Hello,
pimi <madalinionel.patrascu@mdc-berlin.de> skribis:
> * gnu/packages/bioinformatics.scm (filtlong): New variable.
Applied with the changes below; let me know if anything is amiss.
Thanks!
Ludo’.
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diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 43cdf811e..ed713cd14 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14076,7 +14076,6 @@ absolute GSEA.")
(file-name (git-file-name name version))
(sha256
(base32 "1xr92r820x8qlkcr3b57iw223yq8vjgyi42jr79w2xgw47qzr575"))))
- ;;(properties `((upstream-name . "Filtlong")))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no check target
@@ -14087,9 +14086,7 @@ absolute GSEA.")
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
- (scripts (string-append out "/scripts")))
- (mkdir-p bin)
- (mkdir-p scripts)
+ (scripts (string-append out "/share/filtlong/scripts")))
(install-file "bin/filtlong" bin)
(install-file "scripts/histogram.py" scripts)
(install-file "scripts/read_info_histograms.sh" scripts))
@@ -14098,8 +14095,8 @@ absolute GSEA.")
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(path (getenv "PYTHONPATH")))
- ;;(wrap-program (string-apend scripts "scripts/read_info_histograms.sh")
- (wrap-program (string-append out "/scripts/histogram.py")
+ (wrap-program (string-append out
+ "/share/filtlong/scripts/histogram.py")
`("PYTHONPATH" ":" prefix (,path))))
#t))
(add-before 'check 'patch-tests
@@ -14114,7 +14111,7 @@ absolute GSEA.")
(home-page "https://github.com/rrwick/Filtlong/")
(synopsis "Tool for quality filtering of Nanopore and PacBio data")
(description
- "The @code{filtlong} package is a tool for filtering long reads by quality.
+ "The Filtlong package is a tool for filtering long reads by quality.
It can take a set of long reads and produce a smaller, better subset. It uses
both read length (longer is better) and read identity (higher is better) when
choosing which reads pass the filter.")
next prev parent reply other threads:[~2018-10-08 16:33 UTC|newest]
Thread overview: 5+ messages / expand[flat|nested] mbox.gz Atom feed top
2018-10-08 9:17 [bug#32984] [PATCH] gnu: Add filtlong pimi
2018-10-08 16:32 ` Ludovic Courtès [this message]
2018-10-09 16:22 ` [bug#32984] [PATCH] gnu: filtlong: update path in aux script pimi
2018-10-11 20:55 ` Leo Famulari
2018-11-05 16:26 ` mpatras
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