Andreas Tille pushed to branch master at Debian Med / mcl
Commits: e11c1bdb by Andreas Tille at 2022-11-16T15:12:09+01:00 Move external code in a separate subdirectory - - - - - 5 changed files: - debian/changelog - debian/mcl.install - + debian/mcl_14-137_scripts/README - + debian/mcl_14-137_scripts/mclblastline - debian/mcxdeblast → debian/mcl_14-137_scripts/mcxdeblast Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,9 @@ +mcl (1:22-282+ds-3) UNRELEASED; urgency=medium + + * Move external code in a separate subdirectory + + -- Andreas Tille <[email protected]> Wed, 16 Nov 2022 15:11:45 +0100 + mcl (1:22-282+ds-2) unstable; urgency=medium * Team Upload. ===================================== debian/mcl.install ===================================== @@ -1,4 +1,4 @@ usr/bin -debian/mcxdeblast usr/bin -scripts/clx* usr/share/doc/mcl/scripts -scripts/minimcl usr/share/doc/mcl/scripts +debian/mcl_14-137_scripts/mcxdeblast usr/bin +scripts/clx* usr/share/doc/mcl/scripts +scripts/minimcl usr/share/doc/mcl/scripts ===================================== debian/mcl_14-137_scripts/README ===================================== @@ -0,0 +1 @@ +These scripts are copied from mcl-14-137 in dir src/alien/oxygen/src ===================================== debian/mcl_14-137_scripts/mclblastline ===================================== @@ -0,0 +1,58 @@ +#!/usr/bin/env perl + +# Copyright (C) 2003, 2004, 2005, 2006, 2007 Stijn van Dongen + # +# You can redistribute and/or modify this program under the terms of the GNU +# General Public License; either version 3 of the License or (at your option) +# any later version. + +use strict; + +$" = ' '; + +my $do_help = 0; +my $cline = "mclpipeline --parser=mcxdeblast --parser-tag=blast"; + +unless (grep { $_ =~ /^--ass-r[vei]?=/; } @ARGV) { + $cline .= " --ass-r=max"; +} + +$cline .= " @ARGV"; + +if (grep { $_ =~ /--(help|apropos)/; } @ARGV) { + $do_help = 1; +} +elsif (!@ARGV) { + $do_help = 1; + $cline .= " --help"; +} + +if ($do_help) { + print <<_help_; +mcxblastline wraps around the generic mclpipeline script. It fills in the name +of the BLAST parser (mcxdeblast) and the tag ('blast') used to propagate +mcxdeblast options through the pipeline to mcxdeblast itself. You can freely +use all mclpipeline options other than --parser=<executable> and +--parser-tag=<str>. +_help_ +} +if (system $cline) { + print "mcxblastline wrapper: pipeline failed\n"; + print "cline: $cline\n"; + exit(1); +} +if ($do_help) { + print <<_help_; +________________ +The above options are generic pipeline options. You can pass any mcxdeblast +option by inserting the 'blast' tag in front of that particular option. For +example, the mcxdeblast --score=x option (where x is 'b' or 'e') should +be passed to mcxblastline as --blast-score=x. + +The mcxdeblast --xo-dat option is special; it must *not* be prefixed, as it is +shared with mclpipeline, as can be seen from the above listing. The mcxdeblast +--xi-dat option should not be used, as it encapsulated by the mclpipeline --xi +option. +_help_ +} + ===================================== debian/mcxdeblast → debian/mcl_14-137_scripts/mcxdeblast ===================================== View it on GitLab: https://salsa.debian.org/med-team/mcl/-/commit/e11c1bdb7eb4b9ff4bfab26bf0a9efe6c5c9da89 -- View it on GitLab: https://salsa.debian.org/med-team/mcl/-/commit/e11c1bdb7eb4b9ff4bfab26bf0a9efe6c5c9da89 You're receiving this email because of your account on salsa.debian.org.
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