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bug#32984: [PATCH] gnu: Add filtlong.
From: |
Ludovic Courtès |
Subject: |
bug#32984: [PATCH] gnu: Add filtlong. |
Date: |
Mon, 08 Oct 2018 18:32:06 +0200 |
User-agent: |
Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) |
Hello,
pimi <address@hidden> skribis:
> * gnu/packages/bioinformatics.scm (filtlong): New variable.
Applied with the changes below; let me know if anything is amiss.
Thanks!
Ludo’.
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.")