[med-svn] [Git][med-team/mcl][master] Move external code in a separate subdirectory

[Andreas Tille (@tille)]

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 <tille at debian.org>  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
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