[med-svn] [Git][med-team/stacks][master] 5 commits: New upstream version 2.53+dfsg

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / stacks


Commits:
509bbff5 by Steffen Moeller at 2020-04-26T01:39:31+02:00
New upstream version 2.53+dfsg
- - - - -
d6a65fe5 by Steffen Moeller at 2020-04-26T01:39:31+02:00
routine-update: New upstream version

- - - - -
97e22784 by Steffen Moeller at 2020-04-26T01:39:32+02:00
Update upstream source from tag 'upstream/2.53+dfsg'

Update to upstream version '2.53+dfsg'
with Debian dir cf09378c22f5f97fdc9c99c815431a6782a99f47
- - - - -
2c62e2d5 by Steffen Moeller at 2020-04-26T01:45:50+02:00
routine-update: Ready to upload to unstable

- - - - -
7df2bfc5 by Steffen Moeller at 2020-04-26T01:57:04+02:00
Ready to upload.

- - - - -


8 changed files:

- ChangeLog
- configure.ac
- debian/changelog
- debian/control
- + debian/patches/RisR.patch
- debian/patches/series
- debian/upstream/metadata
- scripts/denovo_map.pl


Changes:

=====================================
ChangeLog
=====================================
@@ -1,3 +1,7 @@
+Stacks 2.53 - March 28, 2020
+----------------------------
+    Bugfix: denovo_map.pl was broken for running cstacks on non-genetic map datasets.
+
 Stacks 2.52 - March 5, 2020
 ---------------------------
     Feature: denovo_map.pl now has a --resume options, which will restart the pipeline if a previous run failed


=====================================
configure.ac
=====================================
@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ(2.59)
-AC_INIT([Stacks], [2.52])
+AC_INIT([Stacks], [2.53])
 AC_CONFIG_AUX_DIR([config])
 AM_INIT_AUTOMAKE([-Wall -Werror foreign parallel-tests subdir-objects])
 AC_CONFIG_SRCDIR([src/ustacks.cc])


=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+stacks (2.53+dfsg-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * Updated bio.tools entry to lower-case
+  * Added dependency on littler to allow execution
+    of R script
+
+ -- Steffen Moeller <moeller at debian.org>  Sun, 26 Apr 2020 01:41:49 +0200
+
 stacks (2.52+dfsg-1) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -23,7 +23,8 @@ Depends: ${shlibs:Depends},
          samtools,
          libdbi-perl
 Recommends: libspreadsheet-writeexcel-perl,
-            python3
+            python3,
+            littler
 Conflicts: stacks-web
 Provides: stacks-web
 Replaces: stacks-web


=====================================
debian/patches/RisR.patch
=====================================
@@ -0,0 +1,10 @@
+Index: stacks/scripts/stacks-hist2d-loci-samples-coverage
+===================================================================
+--- stacks.orig/scripts/stacks-hist2d-loci-samples-coverage
++++ stacks/scripts/stacks-hist2d-loci-samples-coverage
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env Rscript
++#!/usr/bin/r
+ 
+ usage = "\
+ usage: stacks-hist2d-loci-samples-coverage reads_per_sample_per_locus.tsv


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
+RisR.patch
 script-exe-paths
 use_debian_packaged_htslib.patch
 2to3.patch


=====================================
debian/upstream/metadata
=====================================
@@ -19,4 +19,4 @@ Registry:
  - Name: conda:bioconda
    Entry: stacks
  - Name: bio.tools
-   Entry: Stacks
+   Entry: stacks


=====================================
scripts/denovo_map.pl
=====================================
@@ -571,8 +571,8 @@ sub parse_population_map {
     #
     my @k = keys %{$pops};
     if (scalar(@k) == 2) {
-        if ( ($k[0] == "parent"  and $k[1] == "progeny") or
-             ($k[0] == "progent" and $k[1] == "parent") ) {
+        if ( ($k[0] eq "parent"  && $k[1] eq "progeny") ||
+             ($k[0] eq "progeny" && $k[1] eq "parent") ) {
             print STDERR "Genetic map detected from population map, only 'parent' samples will be loaded into the catalog.\n";
             $$map = true;
         }



View it on GitLab: https://salsa.debian.org/med-team/stacks/-/compare/3c13ab827dffd2dbfa6ba26be491f5261e8fe4eb...7df2bfc5e945406aceb414a3c25b928aea76c2ed

-- 
View it on GitLab: https://salsa.debian.org/med-team/stacks/-/compare/3c13ab827dffd2dbfa6ba26be491f5261e8fe4eb...7df2bfc5e945406aceb414a3c25b928aea76c2ed
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200425/6458a242/attachment-0001.html>