From unknown Sun Aug 17 10:26:20 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#32984] [PATCH] gnu: Add filtlong. 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Mon, 8 Oct 2018 11:17:58 +0200 (CEST) Received: from biadmin-KVM.nat (141.80.113.106) by SW-IT-P-CAS4.mdc-berlin.net (141.80.113.59) with Microsoft SMTP Server (TLS) id 14.3.408.0; Mon, 8 Oct 2018 11:17:58 +0200 From: pimi Date: Mon, 8 Oct 2018 11:17:41 +0200 Message-ID: <20181008091741.31531-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.17.1 MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.5.1010-24142.005 X-TM-AS-Result: No-3.233700-8.000000-10 X-TMASE-MatchedRID: WO6FSsaLhY17qToVEfwBPAPZZctd3P4BWwKGivsEuI0JwzIPHDjusTIr zgmosr50Utir88BGn9mlfFENwMmeknH0SatXLU38i3TrOhAURKEW2bKZUhvEuif6nnnZywjVYHk 3pEJdwIemlHbHSFj7vqJdLEWoW1FxkTgVTZl1A7iRGzV8Bxg0cVT5iq0BT4XZu+YsotvHgsQ5d9 n04fLNZhvDAwdNITUfIDMCZJXrGw+tuHmXLC26Q1z+axQLnAVB+nvSwfDbaCXOxDyJFXIPjnATZ xYeb66AMSNWuP5JTyKTyW8AYjos4AzyMxeMEX6wFEUknJ/kEl5IquHKOC7ooRe9CQaLe2PP9xS3 mVzWUuAojN1lLei7RUUGTufPThW7MucBy0s445//XOjULa9OnOrMsz67YtZA14zbY/QYPQnFI4t 73s/l7oiKFFSh4L/H1qdA16+EkzWtJmHrjt29uhXit6adbGJ96I9i8/RYrOUaPzUimjy38l5lID EGwLye X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.233700-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.5.1010-24142.005 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -4.4 (----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.4 (-----) * gnu/packages/bioinformatics.scm (filtlong): New variable. --- gnu/packages/bioinformatics.scm | 63 +++++++++++++++++++++++++++++++++ 1 file changed, 63 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ab9dc185a..43cdf811e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14057,3 +14057,66 @@ absolute GSEA.") (description "Ngless is a domain-specific language for @dfn{next-generation sequencing} (NGS) data processing.") (license license:expat))) + +(define-public filtlong + ;; The recommended way to install is to clone the git repository + ;; https://github.com/rrwick/Filtlong#installation + ;; and the lastest release is more than nine months old + (let ((commit "d1bb46dfe8bc7efe6257b5ce222c04bfe8aedaab") + (revision "1")) + (package + (name "filtlong") + (version (git-version "0.2.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rrwick/Filtlong.git") + (commit commit))) + (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 + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'install + (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) + (install-file "bin/filtlong" bin) + (install-file "scripts/histogram.py" scripts) + (install-file "scripts/read_info_histograms.sh" scripts)) + #t)) + (add-after 'install 'wrap-program + (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") + `("PYTHONPATH" ":" prefix (,path)))) + #t)) + (add-before 'check 'patch-tests + (lambda _ + (substitute* "scripts/read_info_histograms.sh" + (("awk") (which "gawk"))) + #t))))) + (inputs + `(("gawk" ,gawk) ;for read_info_histograms.sh + ("python" ,python-2) ; required for histogram.py + ("zlib" ,zlib))) + (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. +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.") + (license (list license:gpl3 ;filtlong + license:asl2.0))))) ;histogram.py -- 2.17.1 From unknown Sun Aug 17 10:26:20 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: pimi Subject: bug#32984: closed (Re: [bug#32984] [PATCH] gnu: Add filtlong.) Message-ID: References: <87murowgah.fsf@gnu.org> <20181008091741.31531-1-madalinionel.patrascu@mdc-berlin.de> X-Gnu-PR-Message: they-closed 32984 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 32984@debbugs.gnu.org Date: Mon, 08 Oct 2018 16:33:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1539016382-24254-1" This is a multi-part message in MIME format... ------------=_1539016382-24254-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #32984: [PATCH] gnu: Add filtlong. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 32984@debbugs.gnu.org. --=20 32984: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D32984 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1539016382-24254-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 32984-done) by debbugs.gnu.org; 8 Oct 2018 16:32:36 +0000 Received: from localhost ([127.0.0.1]:40700 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1g9YSS-0006IH-12 for submit@debbugs.gnu.org; Mon, 08 Oct 2018 12:32:36 -0400 Received: from eggs.gnu.org ([208.118.235.92]:41554) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1g9YSQ-0006I5-QD for 32984-done@debbugs.gnu.org; Mon, 08 Oct 2018 12:32:35 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1g9YSE-0001Ba-RT for 32984-done@debbugs.gnu.org; Mon, 08 Oct 2018 12:32:27 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:39251) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1g9YS0-00014J-GE; Mon, 08 Oct 2018 12:32:08 -0400 Received: from [193.50.110.78] (port=59918 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1g9YS0-0003T1-3f; Mon, 08 Oct 2018 12:32:08 -0400 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: pimi Subject: Re: [bug#32984] [PATCH] gnu: Add filtlong. 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> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 32984-done Cc: ricardo.wurmus@mdc-berlin.de, 32984-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -6.0 (------) --=-=-= 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.") --=-=-=-- ------------=_1539016382-24254-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 8 Oct 2018 09:18:30 +0000 Received: from localhost ([127.0.0.1]:39898 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1g9RgM-00052w-CH for submit@debbugs.gnu.org; Mon, 08 Oct 2018 05:18:30 -0400 Received: from eggs.gnu.org ([208.118.235.92]:57630) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1g9RgK-00052i-Qn for submit@debbugs.gnu.org; Mon, 08 Oct 2018 05:18:29 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1g9Rg6-0007xX-L3 for submit@debbugs.gnu.org; Mon, 08 Oct 2018 05:18:23 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:44580) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1g9Rg4-0007wb-Et for submit@debbugs.gnu.org; Mon, 08 Oct 2018 05:18:14 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:39001) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1g9Rg3-000138-8c for guix-patches@gnu.org; Mon, 08 Oct 2018 05:18:12 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1g9Rg0-0007v4-44 for guix-patches@gnu.org; Mon, 08 Oct 2018 05:18:11 -0400 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:34800) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1g9Rfz-0007sH-LW for guix-patches@gnu.org; Mon, 08 Oct 2018 05:18:08 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id 56B491393D63 for ; Mon, 8 Oct 2018 11:18:04 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:x-mailer:message-id:date :date:subject:subject:from:from:received:received:received; s= mdc; t=1538990279; x=1540804680; bh=fBubiozWag6LqPvfQyO2+6ZT1ewy d4dv5imOmx9KGRc=; b=DJyc1rVz2LzknutUfT7EAlvaNZvZNX+RCVsOEC1lZYF1 loyvo0e/7qnysaFtnhSa7lhc1aixFKQ6X6Z5kU1UqHsKANIhcf4kqkgst9wK/MFb h/NrSaMQFQgOHudrHDV6vrq53kl8yfPQIgg9KVOVnoLuoSqp04OtxFRt1EpqXgI= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 89JVayJ_UHq7 for ; Mon, 8 Oct 2018 11:17:59 +0200 (CEST) Received: from SW-IT-P-CAS4.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-SHA384 (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS for ; Mon, 8 Oct 2018 11:17:58 +0200 (CEST) Received: from biadmin-KVM.nat (141.80.113.106) by SW-IT-P-CAS4.mdc-berlin.net (141.80.113.59) with Microsoft SMTP Server (TLS) id 14.3.408.0; Mon, 8 Oct 2018 11:17:58 +0200 From: pimi To: Subject: [PATCH] gnu: Add filtlong. Date: Mon, 8 Oct 2018 11:17:41 +0200 Message-ID: <20181008091741.31531-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.17.1 MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.5.1010-24142.005 X-TM-AS-Result: No-3.233700-8.000000-10 X-TMASE-MatchedRID: WO6FSsaLhY17qToVEfwBPAPZZctd3P4BWwKGivsEuI0JwzIPHDjusTIr zgmosr50Utir88BGn9mlfFENwMmeknH0SatXLU38i3TrOhAURKEW2bKZUhvEuif6nnnZywjVYHk 3pEJdwIemlHbHSFj7vqJdLEWoW1FxkTgVTZl1A7iRGzV8Bxg0cVT5iq0BT4XZu+YsotvHgsQ5d9 n04fLNZhvDAwdNITUfIDMCZJXrGw+tuHmXLC26Q1z+axQLnAVB+nvSwfDbaCXOxDyJFXIPjnATZ xYeb66AMSNWuP5JTyKTyW8AYjos4AzyMxeMEX6wFEUknJ/kEl5IquHKOC7ooRe9CQaLe2PP9xS3 mVzWUuAojN1lLei7RUUGTufPThW7MucBy0s445//XOjULa9OnOrMsz67YtZA14zbY/QYPQnFI4t 73s/l7oiKFFSh4L/H1qdA16+EkzWtJmHrjt29uhXit6adbGJ96I9i8/RYrOUaPzUimjy38l5lID EGwLye X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.233700-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.5.1010-24142.005 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -4.4 (----) X-Debbugs-Envelope-To: submit Cc: ricardo.wurmus@mdc-berlin.de, pimi X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.4 (-----) * gnu/packages/bioinformatics.scm (filtlong): New variable. --- gnu/packages/bioinformatics.scm | 63 +++++++++++++++++++++++++++++++++ 1 file changed, 63 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ab9dc185a..43cdf811e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14057,3 +14057,66 @@ absolute GSEA.") (description "Ngless is a domain-specific language for @dfn{next-generation sequencing} (NGS) data processing.") (license license:expat))) + +(define-public filtlong + ;; The recommended way to install is to clone the git repository + ;; https://github.com/rrwick/Filtlong#installation + ;; and the lastest release is more than nine months old + (let ((commit "d1bb46dfe8bc7efe6257b5ce222c04bfe8aedaab") + (revision "1")) + (package + (name "filtlong") + (version (git-version "0.2.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rrwick/Filtlong.git") + (commit commit))) + (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 + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'install + (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) + (install-file "bin/filtlong" bin) + (install-file "scripts/histogram.py" scripts) + (install-file "scripts/read_info_histograms.sh" scripts)) + #t)) + (add-after 'install 'wrap-program + (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") + `("PYTHONPATH" ":" prefix (,path)))) + #t)) + (add-before 'check 'patch-tests + (lambda _ + (substitute* "scripts/read_info_histograms.sh" + (("awk") (which "gawk"))) + #t))))) + (inputs + `(("gawk" ,gawk) ;for read_info_histograms.sh + ("python" ,python-2) ; required for histogram.py + ("zlib" ,zlib))) + (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. +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.") + (license (list license:gpl3 ;filtlong + license:asl2.0))))) ;histogram.py -- 2.17.1 ------------=_1539016382-24254-1-- From unknown Sun Aug 17 10:26:20 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#32984] [PATCH] gnu: filtlong: update path in aux script. References: <20181008091741.31531-1-madalinionel.patrascu@mdc-berlin.de> In-Reply-To: <20181008091741.31531-1-madalinionel.patrascu@mdc-berlin.de> Resent-From: pimi Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 09 Oct 2018 16:24:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 32984 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <32984@debbugs.gnu.org> Cc: pimi Received: via spool by 32984-submit@debbugs.gnu.org id=B32984.153910219018678 (code B ref 32984); Tue, 09 Oct 2018 16:24:01 +0000 Received: (at 32984) by debbugs.gnu.org; 9 Oct 2018 16:23:10 +0000 Received: from localhost ([127.0.0.1]:42497 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1g9umr-0004rB-VC for submit@debbugs.gnu.org; Tue, 09 Oct 2018 12:23:10 -0400 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:49086) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1g9umq-0004r3-11 for 32984@debbugs.gnu.org; Tue, 09 Oct 2018 12:23:08 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id F0E17139920B for <32984@debbugs.gnu.org>; Tue, 9 Oct 2018 18:23:06 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:x-mailer:message-id:date :date:subject:subject:from:from:received:received:received; s= mdc; t=1539102181; x=1540916582; bh=O8ewZX1VKkP4y2y587dKh6ZLV2OS +8Ud0WWe93yRT7g=; b=oz8xPOZAgdrh/jXFOzph18FnihaKc4YtapAYvoghc5f6 cNfqyVztzdpNs+glEllVGExDCVkVlcBR4IwIaHeqHXNOloRpHbu69z1hHalps/OI ErhW7UOvvtpnF4sUI99c70YL5XpTbLGZ4KepfGLUopZ6fuLoEOmkY3IKZGR/UzU= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 4tcPokIfZMUe for <32984@debbugs.gnu.org>; Tue, 9 Oct 2018 18:23:01 +0200 (CEST) Received: from SW-IT-P-CAS2.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-SHA384 (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS for <32984@debbugs.gnu.org>; Tue, 9 Oct 2018 18:23:01 +0200 (CEST) Received: from biadmin-KVM.nat (141.80.113.106) by SW-IT-P-CAS2.mdc-berlin.net (141.80.113.54) with Microsoft SMTP Server (TLS) id 14.3.408.0; Tue, 9 Oct 2018 18:23:01 +0200 From: pimi Date: Tue, 9 Oct 2018 18:22:39 +0200 Message-ID: <20181009162239.17415-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.17.1 MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.5.1010-24146.001 X-TM-AS-Result: No-1.941200-8.000000-10 X-TMASE-MatchedRID: /KgKPWMniwypTcMRueXmIjAdpuStCriJVjkEEmuL2x3VU2WiOk7jaC8s MR89db4U4vM1YF6AJbZhyT3WNjppUtAtbEEX0MxBxEHRux+uk8jfhP1xgyx3DBcg2jNczidExsO /7jHFdkNBHz07jBpmZFJZwca8z9zUSZCqSJm1Rkpv4iCLbg6roIVHOeiIev7EVIC/lNN/4ChmhG Z0ywn81YISrdkIFqeuO4Y2dUBhL/BTBYT7RGXoWxJAEJH0NuHT9aAnbWsWzHc= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.941200-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.5.1010-24146.001 X-Spam-Score: -0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * gnu/packages/bioinformatics.scm (filtlong)[extra scritps]: corrected the loading path for the filtlong in the script read_info_histograms.sh. --- gnu/packages/bioinformatics.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ed713cd14..cb9ce4df0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14103,6 +14103,8 @@ absolute GSEA.") (lambda _ (substitute* "scripts/read_info_histograms.sh" (("awk") (which "gawk"))) + (substitute* "scripts/read_info_histograms.sh" + (("/../") "/../../../")) #t))))) (inputs `(("gawk" ,gawk) ;for read_info_histograms.sh -- 2.17.1 From unknown Sun Aug 17 10:26:20 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#32984] [PATCH] gnu: filtlong: update path in aux script. Resent-From: Leo Famulari Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 11 Oct 2018 20:56:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 32984 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: pimi Cc: 32984@debbugs.gnu.org Received: via spool by 32984-submit@debbugs.gnu.org id=B32984.15392913579709 (code B ref 32984); Thu, 11 Oct 2018 20:56:01 +0000 Received: (at 32984) by debbugs.gnu.org; 11 Oct 2018 20:55:57 +0000 Received: from localhost ([127.0.0.1]:45571 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gAhzx-0002WX-La for submit@debbugs.gnu.org; Thu, 11 Oct 2018 16:55:57 -0400 Received: from wout1-smtp.messagingengine.com ([64.147.123.24]:40609) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gAhzv-0002WN-Nu for 32984@debbugs.gnu.org; Thu, 11 Oct 2018 16:55:56 -0400 Received: from compute4.internal (compute4.nyi.internal [10.202.2.44]) by mailout.west.internal (Postfix) with ESMTP id 9A224C6B; Thu, 11 Oct 2018 16:55:54 -0400 (EDT) Received: from mailfrontend2 ([10.202.2.163]) by compute4.internal (MEProxy); Thu, 11 Oct 2018 16:55:54 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=famulari.name; h=date:from:to:cc:subject:message-id:references:mime-version :content-type:in-reply-to; s=mesmtp; bh=XJ85x63IVq3MzrJvlPra5XUy 9nQi67ffhpG7LIzJYho=; b=H2qQ9oNd89ybuHV8OkGByT5jNx+KhGMWNL309mQD B+kXE0e8jXMoIsm1TRLCbVIZjFqRopWKZquyg1JVaZwg1PNHb/IiWBoz/lbOjwIO AebiQw+vDTDAJKz1Rlaa/RTILWxdbMxkP1GD/3R594qkQIDZiEgEJxEwbFhHDPp+ 7iE= DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d= messagingengine.com; h=cc:content-type:date:from:in-reply-to :message-id:mime-version:references:subject:to:x-me-proxy :x-me-proxy:x-me-sender:x-me-sender:x-sasl-enc; s=fm1; bh=XJ85x6 3IVq3MzrJvlPra5XUy9nQi67ffhpG7LIzJYho=; b=A4CyDogtKbfmAIhbJ2A+2L 9hVphU1pL6igvbRC6wCb8LH+aPuhsDuN9jROjHZ07CCeuXPVoxXzn88WZQAWjE+B s3zu2wQvSzWA/MWse1Vic9p7CkArpyJBQx13HDNMwYbCrDUrl00iIT6TUQnisZTF yrtvoV6ToiawMoj9BkIG8X71ruUiwslh5FL6F2RDvkqPVwooRt0HnSZ4FpYYPdbe 3C1MfRFJVaMI3rlIgSbyXThKnUXPFQYeCIQb7Lc/P3HJQrFGRmwt4k44ZCdNnvoN 4yOuzKYL+A8xWPGhK54SK0kctH3tWNM2J5+SOiWI9COMO/TNOKcDlJ8nWh67v10w == X-ME-Sender: X-ME-Proxy: Received: from localhost (unknown [172.58.224.212]) by mail.messagingengine.com (Postfix) with ESMTPA id 40050102D7; Thu, 11 Oct 2018 16:55:51 -0400 (EDT) Date: Thu, 11 Oct 2018 16:55:50 -0400 From: Leo Famulari Message-ID: <20181011205550.GF7201@jasmine.lan> References: <20181008091741.31531-1-madalinionel.patrascu@mdc-berlin.de> <20181009162239.17415-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha256; protocol="application/pgp-signature"; boundary="iBwuxWUsK/REspAd" Content-Disposition: inline In-Reply-To: <20181009162239.17415-1-madalinionel.patrascu@mdc-berlin.de> User-Agent: Mutt/1.10.1 (2018-07-13) X-Spam-Score: -0.7 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.7 (-) --iBwuxWUsK/REspAd Content-Type: text/plain; charset=us-ascii Content-Disposition: inline On Tue, Oct 09, 2018 at 06:22:39PM +0200, pimi wrote: > * gnu/packages/bioinformatics.scm (filtlong)[extra scritps]: corrected > the loading path for the filtlong in the script read_info_histograms.sh. [...] > (lambda _ > (substitute* "scripts/read_info_histograms.sh" > (("awk") (which "gawk"))) > + (substitute* "scripts/read_info_histograms.sh" > + (("/../") "/../../../")) > #t))))) Can you add a code comment explaining the effect of this change? It's rather cryptic! :) --iBwuxWUsK/REspAd Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAABCAAdFiEEsFFZSPHn08G5gDigJkb6MLrKfwgFAlu/uNYACgkQJkb6MLrK fwhh6BAAsigRcAvjpZVDfxLVWsbYp4cruZdTIlUlBpTAl61K1bTfrpbHX5B53tKW 2BgjEUsMTXD4DU1QHuOxudgOdhCt4/FJHT+WP2PeJPzynmN5sBp7tmfElewTlHIy YfGb5WjONI8pbmsEgMxqI6IMGiyHiW66DRpm0YMvs3pLTqGKa+TIAPTlgOHkkAsP P71b7kSDMBnLfrdhEoxi9L6dSuAcCj/vG2+JvCyomuFpUymRi4D6+dZWx8bXVr8t sNhGiB5EJbrFq74w4SOG3dUPrQFMXvS09J1UnUP2N/ESqQRsJDfkmL/XzaqXXwBE amCsSRxCCS6bA+hBQlxMp4K4gac+/NMDin4J5uhGpC7aXDDWxisq1NKOSeAC4w0k ntYz48UIjP/qxzmoPBaQ7uNfzOUu+yiqjM6w6+JJG7kN+jL7qdfpkc+dEiIsf8s9 5PCqwXb/8kNoTWydCbVEqcs617XIy4UY70MAH7MMv463XiiDSlm3JKLT3NOZ4HCx c+VlzGKo4/AkcY2oFeuFYKdGQvNPHWLSnO21ePHy2tGpmCDWPAIAQfKocHVo14+y knWQ8EuJRQCorlxCqiBZGpgMSMTkAKnJziucV7TUS6OEi7Rn5baCdVPHmP6aEbna OwmZ32+5qDfapKYmBY8qL2RZXfWkWilXZlrH9PPloBvPhDWNBVs= =wQe2 -----END PGP SIGNATURE----- --iBwuxWUsK/REspAd-- From unknown Sun Aug 17 10:26:20 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#32984] [PATCH] gnu: filtlong: update path in aux script. Resent-From: mpatras Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 05 Nov 2018 16:27:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 32984 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Leo Famulari Cc: 32984@debbugs.gnu.org Received: via spool by 32984-submit@debbugs.gnu.org id=B32984.154143520019002 (code B ref 32984); Mon, 05 Nov 2018 16:27:02 +0000 Received: (at 32984) by debbugs.gnu.org; 5 Nov 2018 16:26:40 +0000 Received: from localhost ([127.0.0.1]:35492 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gJhi4-0004wQ-GF for submit@debbugs.gnu.org; Mon, 05 Nov 2018 11:26:40 -0500 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:49020) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gJhi2-0004wI-U3 for 32984@debbugs.gnu.org; Mon, 05 Nov 2018 11:26:39 -0500 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id D132EB8F493; Mon, 5 Nov 2018 17:26:37 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-language:content-type:content-type:in-reply-to :mime-version:user-agent:date:date:message-id:from:from :references:subject:subject:received:received:received; s=mdc; t=1541435192; x=1543249593; bh=Aj0NNInfAQjyUANXdY/RrdT+vTj6IQ+p Jr5tZQQq4JI=; b=faBYVOG86/A4LBH4wR4r+J0JV3joqeJskMVMh81dvZpOPmZc S1MV9UqqYoVM32UQNvJggSwBawzIdNcaMxz1iUdWqiYsdWZK93IWqE9ELOA5K6ct hijx9dDrc9HlpRpO9C0ILVaeVLD4uuaIZ7J5wao0tUDCqYl1FXzkpEG2MtU= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from pegasus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (pegasus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id rT8S8LtSIYIj; Mon, 5 Nov 2018 17:26:32 +0100 (CET) Received: from SW-IT-P-CAS2.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-SHA384 (256/256 bits)) (No client certificate requested) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTPS; Mon, 5 Nov 2018 17:26:31 +0100 (CET) Received: from [141.80.245.185] (141.80.245.185) by SW-IT-P-CAS2.mdc-berlin.net (141.80.113.54) with Microsoft SMTP Server (TLS) id 14.3.408.0; Mon, 5 Nov 2018 17:26:12 +0100 References: <20181008091741.31531-1-madalinionel.patrascu@mdc-berlin.de> <20181009162239.17415-1-madalinionel.patrascu@mdc-berlin.de> <20181011205550.GF7201@jasmine.lan> From: mpatras Message-ID: <92b28f6e-4a68-5b5f-dcb7-40c376774f22@mdc-berlin.de> Date: Mon, 5 Nov 2018 17:26:12 +0100 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:60.0) Gecko/20100101 Thunderbird/60.2.1 MIME-Version: 1.0 In-Reply-To: <20181011205550.GF7201@jasmine.lan> Content-Type: multipart/alternative; boundary="------------895769D193349799FF362945" Content-Language: en-US X-Originating-IP: [141.80.245.185] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.5.1010-24204.001 X-TM-AS-Result: No-3.974500-8.000000-10 X-TMASE-MatchedRID: Jm7Yxmmj9OnsYbGmK/WYxmzBijri5+RV2aYdnwn7qHesafcFLFlU1EJy DX3Q0bQu4bHmO9P2buXWFf2nRol5H5gNyeG1j0t0YwaJXrf2IXQcZd/OW4yvKiBQRBOQhaJi/hB H/uhQMnKWyyXsNfEPjzAED5vkHquaSSQ7jOqms052cLm5pLq1v33/PYNiodjtlQwQKaQE/6WbJx j/y/77pK2e2abXqSOOIyLTOoRClLsIYv24S2K2WI65EQZ6p9MDV6bm0XTx/qFyM+fsO1lvklvfT xRJvtALpEYBIO560crrrT4Oq9+KU4IiDu0n/+6xFKEXM5xicICb/LTS0T1K1lvo8FSqar5S7KBB Z2QBUywZu5/7aPaGbWjN205Cw2eJ2ygMnPk4DNxwvDydhBUuyDWBEYnpSn2FmnnIaNaZOLEwDK3 q7PoI7PZZckY8QOMipP78tAXYZqXvCC3jhHjcj8g6fo0rxLVrJd2n2XoSRFnnZVNiuSZvWzXJwP /7hrMsWFQNk4+HCoj/voIzhn8wZuVHGbcDbAq6gxsfzkNRlfKtIWznhjjBtTBqYATSOgWjAQeyR axckBRI8g82Y3R7ZTrJVlx3BMcKMWGpJHZXss8BNtYyd4f6JF5bq9mG2SXCgNX2a60rKxk50y+G fo3gSfo75oN+aNzqJMif33HjSozFHs16nUDxt++JuDPAZnHWy5dzqJJIF1XktlmOXXTSnLQisFQ Pfmoc+crICkOzqvho8XToPf/MOR6KOj2ARplb X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.974500-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.5.1010-24204.001 X-Spam-Score: -5.0 (-----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -6.0 (------) --------------895769D193349799FF362945 Content-Type: text/plain; charset="UTF-8"; format=flowed Content-Transfer-Encoding: 8bit Hello Leo, I am sorry for this delayed response! In the initial version of this description, I have put the auxiliary scripts in /scripts/. I didn't know that all auxiliary scripts should be put in /share/name_of_package/scripts. The script loads the package using a relative path. Ludo corrected my description and changed my substitute lines to this, - (wrap-program (string-append out "/scripts/histogram.py") + (wrap-program (string-append out + "/share/filtlong/scripts/histogram.py") Now the script is on the right place (/share/filtlong/scripts/histogram.py), but it does not contain the right relative path. So, this patch is needed to correct the relative path. + (substitute* "scripts/read_info_histograms.sh" + (("/../") "/../../../")) Sorry, from the beginning was my mistake! On 11.10.2018 22:55, Leo Famulari wrote: > On Tue, Oct 09, 2018 at 06:22:39PM +0200, pimi wrote: >> * gnu/packages/bioinformatics.scm (filtlong)[extra scritps]: corrected >> the loading path for the filtlong in the script read_info_histograms.sh. > [...] > >> (lambda _ >> (substitute* "scripts/read_info_histograms.sh" >> (("awk") (which "gawk"))) >> + (substitute* "scripts/read_info_histograms.sh" >> + (("/../") "/../../../")) >> #t))))) > Can you add a code comment explaining the effect of this change? It's > rather cryptic! :) -- All the best! Mădălin Ionel Patrașcu System Administrator The Berlin Institute for Medical Systems Biology (BIMSB) Max Delbrück Center (MDC) Robert-Rössle-Straße 10 House 87, room 1.10 13125 Berlin, Germany --------------895769D193349799FF362945 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: 8bit Hello Leo,

I am sorry for this delayed response!

In the initial version of this description, I have put the auxiliary scripts in /scripts/.

I didn't know that all auxiliary scripts should be put in /share/name_of_package/scripts.

The script loads the package using a relative path.

Ludo corrected my description and changed my substitute lines to this,

-                 (wrap-program (string-append out "/scripts/histogram.py")
+                 (wrap-program (string-append out
+                                              "/share/filtlong/scripts/histogram.py")

Now the script is on the right place (/share/filtlong/scripts/histogram.py), but it does not contain the right relative path. So, this patch is needed to correct the relative path.

+               (substitute* "scripts/read_info_histograms.sh"
+                (("/../") "/../../../"))
Sorry, from the beginning was my mistake!
On 11.10.2018 22:55, Leo Famulari wrote:
On Tue, Oct 09, 2018 at 06:22:39PM +0200, pimi wrote:

* gnu/packages/bioinformatics.scm (filtlong)[extra scritps]: corrected
the loading path for the filtlong in the script read_info_histograms.sh.

[...]


              (lambda _
                (substitute* "scripts/read_info_histograms.sh"
                  (("awk") (which "gawk")))
+               (substitute* "scripts/read_info_histograms.sh"
+                (("/../") "/../../../"))
                #t)))))

Can you add a code comment explaining the effect of this change? It's
rather cryptic! :)

-- 
All the best!

Mădălin Ionel Patrașcu

System Administrator
The Berlin Institute for Medical Systems Biology (BIMSB)
Max Delbrück Center (MDC)
Robert-Rössle-Straße 10
House 87, room 1.10
13125 Berlin, Germany
--------------895769D193349799FF362945--