Stacks 2.3 (#13095)

* Stacks update 2.3

* Stacks folder cleanup

* stacks remove 1.47

recipes/stacks/2.3/at.patch

@@ -0,0 +1,71 @@
+# the stacks perl scripts don't work if there is an '@' in the exe_path
+# (where stacks searches for the binaries) this patch sets and ensures that the
+# exe_path is the empty string, i.e. PATH is used (ie conda takes care).
+diff -ruN stacks-2.2-old/scripts/denovo_map.pl stacks-2.2-new/scripts/denovo_map.pl
+--- stacks-2.2/scripts/denovo_map.pl	2018-04-19 18:17:23.000000000 +0200
++++ stacks-2.2/scripts/denovo_map.pl	2019-01-03 08:28:27.174444559 +0100
+@@ -28,7 +28,7 @@
+ use constant false => 0;
+
+ my $dry_run      = false;
+-my $exe_path     = "_BINDIR_";
++my $exe_path     = "";
+ my $out_path     = "";
+ my $popmap_path  = "";
+ my $sample_path  = "";
+@@ -50,13 +50,6 @@
+
+ parse_command_line();
+
+-#
+-# Check for the existence of the necessary pipeline programs
+-#
+-foreach my $prog ("ustacks", "cstacks", "sstacks", "tsv2bam", "gstacks", "populations") {
+-    die "Unable to find '" . $exe_path . $prog . "'.\n" if (!-e $exe_path . $prog);
+-}
+-
+ my ($log, $log_fh, $sample);
+
+ my (@sample_list, %pop_ids, %pops, %grp_ids, %grps, %sample_ids);
+@@ -558,7 +551,6 @@
+         }
+     }
+
+-    $exe_path = $exe_path . "/"          if (substr($exe_path, -1) ne "/");
+     $out_path = substr($out_path, 0, -1) if (substr($out_path, -1) eq "/");
+
+     if (scalar(@parents) > 0 && scalar(@samples) > 0) {
+diff -ruN stacks-2.2-old/scripts/ref_map.pl stacks-2.2-new/scripts/ref_map.pl
+--- stacks-2.2/scripts/ref_map.pl	2018-03-21 15:51:20.000000000 +0100
++++ stacks-2.2/scripts/ref_map.pl	2019-01-03 08:29:17.974257301 +0100
+@@ -28,7 +28,7 @@
+ use constant false => 0;
+
+ my $dry_run      = false;
+-my $exe_path     = "_BINDIR_";
++my $exe_path     = "";
+ my $out_path     = "";
+ my $popmap_path  = "";
+ my $sample_path  = "";
+@@ -47,13 +47,6 @@
+
+ parse_command_line();
+
+-#
+-# Check for the existence of the necessary pipeline programs
+-#
+-foreach my $prog ("gstacks", "populations") {
+-    die "Unable to find '" . $exe_path . $prog . "'.\n" if (!-e $exe_path . $prog);
+-}
+-
+ my ($log, $log_fh, $sample);
+
+ my (@sample_list, %pop_ids, %pops, %grp_ids, %grps, %sample_ids);
+@@ -385,7 +378,6 @@
+         }
+     }
+
+-    $exe_path = $exe_path . "/"          if (substr($exe_path, -1) ne "/");
+     $out_path = substr($out_path, 0, -1) if (substr($out_path, -1) eq "/");
+
+     if (length($popmap_path) == 0) {

recipes/stacks/2.3/build.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+if [[ "$(uname)" == Darwin ]]; then
+    # Fix for install_name_tool error:
+    #   error: install_name_tool: changing install names or rpaths can't be
+    #   redone for: $PREFIX/bin/abyss-overlap (for architecture x86_64) because
+    #   larger updated load commands do not fit (the program must be relinked,
+    #   and you may need to use -headerpad or -headerpad_max_install_names)
+    export LDFLAGS="$LDFLAGS -headerpad_max_install_names"
+fi
+
+export CXXFLAGS="${CXXFLAGS} -std=c++11"
+
+./configure --prefix="$PREFIX" --enable-bam
+make
+make install
+# copy missing scripts
+cp -p scripts/{convert_stacks.pl,extract_interpop_chars.pl} "$PREFIX/bin/"
+
+# fix a bug in ref_map v2.2 is fixed
+sed -i -e "s/_alpha/-alpha/" "$PREFIX"/bin/ref_map.pl
+

recipes/stacks/2.3/conda_build_config.yaml

@@ -0,0 +1,6 @@
+c_compiler:
+  - gcc      # [linux]
+  - clang    # [osx]
+cxx_compiler:
+  - gxx      # [linux]
+  - clangxx  # [osx]

recipes/stacks/2.3/meta.yaml

@@ -0,0 +1,65 @@
+{% set version="2.3" %}
+{% set hash="2a5befaf11ca2f191afcd42a3a3392290d6a116d7fe737b69a2c4d5b77f40c99" %}
+
+package:
+  name: stacks
+  version: {{ version }}
+
+build:
+  number: 3
+
+source:
+  sha256: {{ hash }}
+  url: http://catchenlab.life.illinois.edu/stacks/source/stacks-{{ version }}.tar.gz
+  patches:
+    - at.patch
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+  host:
+    - zlib
+    - openmp  # [linux]
+  run:
+    - perl
+    - perl-bioperl-core
+    - perl-file-spec
+    - perl-file-temp
+    - perl-posix
+    - python >=3
+    - velvet
+    - samtools
+    - zlib
+    - openmp  # [linux]
+
+test:
+  commands:
+    - command -v cstacks
+    - command -v gstacks
+    - command -v sstacks
+    - command -v ustacks
+    - command -v phasedstacks
+    - command -v populations
+    - command -v process_radtags
+    - command -v process_shortreads
+    - command -v clone_filter
+    - command -v kmer_filter
+    - command -v stacks-dist-extract
+    - command -v stacks-integrate-alignments
+    - command -v tsv2bam
+    - command -v convert_stacks.pl
+    - command -v count_fixed_catalog_snps.py
+    - command -v denovo_map.pl
+    - command -v extract_interpop_chars.pl
+    - command -v integrate_alignments.py
+    - command -v ref_map.pl
+
+about:
+  home: http://catchenlab.life.illinois.edu/stacks/
+  license: GPL
+  summary: Stacks is a software pipeline for building loci from RAD-seq
+
+extra:
+  identifiers:
+    - biotools:Stacks
+    - doi:10.1111/mec.12354