From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:4830:134:3::10]:51474) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1g9YSy-0004j9-7N for guix-patches@gnu.org; Mon, 08 Oct 2018 12:33:09 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1g9YSv-0001UO-2W for guix-patches@gnu.org; Mon, 08 Oct 2018 12:33:08 -0400 Received: from debbugs.gnu.org ([208.118.235.43]:36449) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1g9YSs-0001Tp-Ll for guix-patches@gnu.org; Mon, 08 Oct 2018 12:33:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1g9YSs-0006JK-GE for guix-patches@gnu.org; Mon, 08 Oct 2018 12:33:02 -0400 Subject: bug#32984: [PATCH] gnu: Add filtlong. Resent-To: guix-patches@gnu.org Resent-Message-ID: From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) References: <20181008091741.31531-1-madalinionel.patrascu@mdc-berlin.de> Date: Mon, 08 Oct 2018 18:32:06 +0200 In-Reply-To: <20181008091741.31531-1-madalinionel.patrascu@mdc-berlin.de> (pimi's message of "Mon, 8 Oct 2018 11:17:41 +0200") Message-ID: <87murowgah.fsf@gnu.org> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: pimi Cc: ricardo.wurmus@mdc-berlin.de, 32984-done@debbugs.gnu.org --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hello, pimi skribis: > * gnu/packages/bioinformatics.scm (filtlong): New variable. Applied with the changes below; let me know if anything is amiss. Thanks! Ludo=E2=80=99. --=-=-= Content-Type: text/x-patch Content-Disposition: inline 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.") --=-=-=--