Subject: Re: [bug#32984] [PATCH] gnu: Add filtlong.
From: [email-masked] (Ludovic Courtès)
To: pimi <[email-masked]>
Cc: [email-masked], [email-masked]
Date: Mon, 08 Oct 2018 18:32:06 +0200
List-Id: <debbugs-submit.debbugs.gnu.org>

Hello,

pimi <[email-masked]> 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.")