Update Stacks version (#53006)

* Update Stacks version * Remove build file * Update patches * Fix some commands
bioconda · Jan 3, 2025 · 62f656f · 62f656f
1 parent 8ae712f
commit 62f656f
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Showing 6 changed files with 76 additions and 157 deletions.
diff --git a/recipes/stacks/build.sh b/recipes/stacks/build.sh
@@ -14,6 +14,7 @@ export CXXFLAGS="${CXXFLAGS} -std=c++11"
 ./configure --prefix="$PREFIX" --enable-bam
 make
 make install
+
 # copy missing scripts
-sed -i'' '1 s|^.*$|#!/usr/bin/env perl|g' scripts/convert_stacks.pl
-cp -p scripts/{convert_stacks.pl,extract_interpop_chars.pl} "$PREFIX/bin/"
+chmod +x scripts/*.pl
+cp scripts/*.pl "$PREFIX/bin/"
diff --git a/recipes/stacks/build_failure.linux-64.yaml b/recipes/stacks/build_failure.linux-64.yaml
diff --git a/recipes/stacks/kmer_exit.patch b/recipes/stacks/kmer_exit.patch
@@ -1,7 +1,5 @@
-# patch wrong exit codes of kmer filter
-# reported upstream: https://groups.google.com/forum/#!topic/stacks-users/fS3iJOYz6-s
---- src/kmer_filter.cc	2020-07-06 17:23:10.417045722 +0200
-+++ src/kmer_filter.cc	2020-07-06 17:22:54.553176195 +0200
+--- src/kmer_filter.cc.old	2025-01-02 14:40:19.258463783 -0600
++++ src/kmer_filter.cc	2025-01-02 14:41:48.294398484 -0600
 @@ -111,12 +111,12 @@
          if (kmer_distr) {
              generate_kmer_dist(kmers);

diff --git a/recipes/stacks/limits.patch b/recipes/stacks/limits.patch
@@ -1,12 +1,10 @@
-diff -ruN stacks-2.65-org/src/models.h stacks-2.65/src/models.h
---- stacks-2.65-org/src/models.h	2023-10-17 11:57:14.093372152 +0200
-+++ stacks-2.65/src/models.h	2023-10-17 11:57:54.645444150 +0200
-@@ -21,6 +21,8 @@
+--- src/models.h.old	2025-01-02 14:38:48.565528944 -0600
++++ src/models.h	2025-01-02 14:39:32.338497697 -0600
+@@ -21,6 +21,7 @@
  #ifndef __MODELS_H__
  #define __MODELS_H__
 
 +#include <limits>
-+
  #include "constants.h"
  #include "utils.h"
  #include "DNASeq4.h"
diff --git a/recipes/stacks/meta.yaml b/recipes/stacks/meta.yaml
@@ -1,7 +1,9 @@
-{% set version="2.65" %}
-{% set hash="ffd6bd3d6295ab9c89cc451f385d37cd1d47a77019c3d305f31202a2b895e2ea" %}
+{% set name="Stacks" %}
+{% set version="2.68" %}
+{% set sha256="9dc51ea356d60eb4557b0b2d1a8854aafae492aed87f974e0249cc09aa5e7650" %}
+
 package:
-  name: stacks
+  name: {{ name|lower }}
   version: {{ version }}
 
 build:
@@ -11,10 +13,10 @@ build:
     - {{ pin_subpackage("stacks", max_pin="x") }}
 
 source:
-  sha256: {{ hash }}
+  sha256: {{ sha256 }}
   url: https://catchenlab.life.illinois.edu/stacks/source/stacks-{{ version }}.tar.gz
   patches:
-    - at.patch
+    - perl.patches
     - kmer_exit.patch
     - limits.patch
 
@@ -31,7 +33,7 @@ requirements:
     - perl-file-spec
     - perl-file-temp
     - perl-posix
-    - python >=3
+    - python
     - velvet
     - samtools
     - zlib
@@ -40,32 +42,33 @@ requirements:
 
 test:
   commands:
-    - cstacks 2>&1 | grep -Fq 'cstacks {{ version }}'
-    - gstacks 2>&1 | grep -Fq 'gstacks {{ version }}'
-    - sstacks 2>&1 | grep -Fq 'sstacks {{ version }}'
-    - ustacks 2>&1 | grep -Fq 'ustacks {{ version }}'
-    - phasedstacks 2>&1 | grep -Fq 'phasedstacks {{ version }}'
-    - populations 2>&1 | grep -Fq 'populations {{ version }}'
-    - process_radtags 2>&1 | grep -Fq 'process_radtags {{ version }}'
-    - process_shortreads 2>&1 | grep -Fq 'process_shortreads {{ version }}'
-    - clone_filter 2>&1 | grep -Fq 'clone_filter {{ version }}'
-    - kmer_filter 2>&1 | grep -Fq 'kmer_filter {{ version }}'
-    - stacks-dist-extract 2>&1 | grep -q Usage
-    - tsv2bam 2>&1 | grep -Fq 'tsv2bam {{ version }}'
-    - convert_stacks.pl 2>&1 | grep -Fq 'convert_stacks.pl _VERSION_'
-    - denovo_map.pl -h 2>&1 | grep -Fq 'denovo_map.pl {{ version }}'
-    - extract_interpop_chars.pl -h 2>&1 | grep -Fq 'extract-interpop-chars.pl'
-    - stacks-integrate-alignments 2>&1 | grep -Fq usage
-    - ref_map.pl 2>&1 | grep -Fq 'ref_map.pl {{ version }}'
-    - stacks-count-reads-per-sample-per-locus 2>&1 | grep -Fq usage
-    - stacks-hist2d-loci-samples-coverage 2>&1 | grep -Fq usage
-    - stacks-samtools-tview 2>&1 | grep -Fq usage
+    - cstacks 2>&1 | grep "cstacks"
+    - gstacks --help
+    - sstacks 2>&1 | grep "sstacks"
+    - ustacks 2>&1 | grep "ustacks"
+    - phasedstacks 2>&1 | grep "phasedstacks"
+    - populations 2>&1 | grep "populations"
+    - process_radtags 2>&1 | grep "process_radtags"
+    - process_shortreads 2>&1 | grep "process_shortreads"
+    - clone_filter 2>&1 | grep "clone_filter"
+    - kmer_filter 2>&1 | grep "kmer_filter"
+    - stacks-dist-extract --help
+    - tsv2bam --help
+    - convert_stacks.pl -h
+    - denovo_map.pl -h 2>&1 | grep "denovo_map.pl"
+    - extract_interpop_chars.pl -h
+    - stacks-integrate-alignments --help
+    - ref_map.pl 2>&1 | grep "ref_map.pl"
+    - stacks-count-reads-per-sample-per-locus 2>&1 | grep "usage"
+    - stacks-hist2d-loci-samples-coverage 2>&1 | grep "usage"
+    - stacks-samtools-tview 2>&1 | grep "usage"
 
 about:
   home: https://catchenlab.life.illinois.edu/stacks/
-  license: GPL
+  license: GPL-3
+  license_family: GPL3
   license_file: LICENSE
-  summary: Stacks is a software pipeline for building loci from RAD-seq
+  summary: "Stacks is a software pipeline for building loci from short-read sequences."
 
 extra:
   identifiers: