Added new versions for biopet-bamstats (#11571)

recipes/biopet-bamstats/1.0.1/biopet-bamstats.py

@@ -0,0 +1,107 @@
+#!/usr/bin/env python
+#
+# Wrapper script for starting the biopet-bamstats JAR package
+#
+# This script is written for use with the Conda package manager and is copied
+# from the peptide-shaker wrapper. Only the parameters are changed.
+# (https://github.com/bioconda/bioconda-recipes/blob/master/recipes/peptide-shaker/peptide-shaker.py)
+#
+# This file was automatically generated by the sbt-bioconda plugin.
+
+import os
+import subprocess
+import sys
+import shutil
+
+from os import access
+from os import getenv
+from os import X_OK
+
+jar_file = 'BamStats-assembly-1.0.1.jar'
+
+default_jvm_mem_opts = []
+
+# !!! End of parameter section. No user-serviceable code below this line !!!
+
+
+def real_dirname(path):
+    """Return the symlink-resolved, canonicalized directory-portion of path."""
+    return os.path.dirname(os.path.realpath(path))
+
+
+def java_executable():
+    """Return the executable name of the Java interpreter."""
+    java_home = getenv('JAVA_HOME')
+    java_bin = os.path.join('bin', 'java')
+
+    if java_home and access(os.path.join(java_home, java_bin), X_OK):
+        return os.path.join(java_home, java_bin)
+    else:
+        return 'java'
+
+
+def jvm_opts(argv):
+    """Construct list of Java arguments based on our argument list.
+
+    The argument list passed in argv must not include the script name.
+    The return value is a 3-tuple lists of strings of the form:
+      (memory_options, prop_options, passthrough_options)
+    """
+    mem_opts = []
+    prop_opts = []
+    pass_args = []
+    exec_dir = None
+
+    for arg in argv:
+        if arg.startswith('-D'):
+            prop_opts.append(arg)
+        elif arg.startswith('-XX'):
+            prop_opts.append(arg)
+        elif arg.startswith('-Xm'):
+            mem_opts.append(arg)
+        elif arg.startswith('--exec_dir='):
+            exec_dir = arg.split('=')[1].strip('"').strip("'")
+            if not os.path.exists(exec_dir):
+                shutil.copytree(real_dirname(sys.argv[0]), exec_dir, symlinks=False, ignore=None)
+        else:
+            pass_args.append(arg)
+
+    # In the original shell script the test coded below read:
+    #   if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ]
+    # To reproduce the behaviour of the above shell code fragment
+    # it is important to explictly check for equality with None
+    # in the second condition, so a null envar value counts as True!
+
+    if mem_opts == [] and getenv('_JAVA_OPTIONS') is None:
+        mem_opts = default_jvm_mem_opts
+
+    return (mem_opts, prop_opts, pass_args, exec_dir)
+
+
+def main():
+    """
+    PeptideShaker updates files relative to the path of the jar file.
+    In a multiuser setting, the option --exec_dir="exec_dir"
+    can be used as the location for the peptide-shaker distribution.
+    If the exec_dir dies not exist,
+    we copy the jar file, lib, and resources to the exec_dir directory.
+    """
+    java = java_executable()
+    (mem_opts, prop_opts, pass_args, exec_dir) = jvm_opts(sys.argv[1:])
+    jar_dir = exec_dir if exec_dir else real_dirname(sys.argv[0])
+
+    if pass_args != [] and pass_args[0].startswith('eu'):
+        jar_arg = '-cp'
+    else:
+        jar_arg = '-jar'
+
+    jar_path = os.path.join(jar_dir, jar_file)
+
+    java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args
+
+    sys.exit(subprocess.call(java_args))
+
+
+if __name__ == '__main__':
+    main()
+

recipes/biopet-bamstats/1.0.1/build.sh

@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+# Build file is copied from VarScan
+# https://github.com/bioconda/bioconda-recipes/blob/master/recipes/varscan/build.sh
+# This file was automatically generated by the sbt-bioconda plugin.
+
+outdir=$PREFIX/share/$PKG_NAME
+mkdir -p $outdir
+mkdir -p $PREFIX/bin
+cp BamStats-assembly-1.0.1.jar $outdir/BamStats-assembly-1.0.1.jar
+cp $RECIPE_DIR/biopet-bamstats.py $outdir/biopet-bamstats
+ln -s $outdir/biopet-bamstats $PREFIX/bin
+

recipes/biopet-bamstats/1.0.1/meta.yaml

@@ -0,0 +1,69 @@
+# !! THIS FILE WAS AUTOMATICALLY GENERATED BY THE SBT-BIOCONDA PLUGIN !!
+# !!                       DO NOT EDIT MANUALLY                       !!
+
+package:
+  name: biopet-bamstats
+  version: 1.0.1
+source:
+  url: https://github.com/biopet/bamstats/releases/download/v1.0.1/BamStats-assembly-1.0.1.jar
+  sha256: ab1beffd8a5a51e2937cb5efa190d6e57fb8e63d6b19a92e8e83d7db2a9b839e
+build:
+  noarch: generic
+  number: 0
+requirements:
+  run:
+  - openjdk >=8,<9
+  - python
+about:
+  home: https://github.com/biopet/bamstats
+  license: MIT
+  summary: BamStats is a package that contains tools to generate stats from a BAM file, merge those stats for multiple samples, and validate the generated stats files.
+  description: |
+    BamStats is a package that contains tools
+    to generate stats from a BAM file,
+    merge those stats for multiple samples,
+    and validate the generated stats files.
+
+
+    #### Mode - Generate
+
+    Generate reports clipping stats, flag stats, insert size and mapping quality on a BAM file. It outputs
+    a JSON file, but can optionally also output in TSV format.
+
+    The output of the JSON file is organized in a sample - library - readgroup tree structure.
+    If readgroups in the BAM file are not annotated with sample (`SM`) and library (`LB`) tags
+    an error will be thrown.
+    This can be fixed by using `samtools addreplacerg` or `picard AddOrReplaceReadGroups`.
+
+
+    #### Mode - Merge
+
+    This module will merge bamstats files together and keep the sample/library/readgroup structure.
+    Values for the same readgroups will be added.
+    It will also validate the resulting file.
+
+
+    #### Mode - Validate
+
+    Validates a BamStats file.
+    If aggregation values can not be regenerated the file is considered corrupt.
+    This should only happen when the file has been manually edited.
+
+    For documentation and manuals visit our github.io page: https://biopet.github.io/bamstats
+test:
+  commands:
+  - biopet-bamstats merge --help
+  - biopet-bamstats merge --version
+  - biopet-bamstats validate --help
+  - biopet-bamstats validate --version
+  - biopet-bamstats generate --help
+  - biopet-bamstats generate --version
+extra:
+  notes: |
+    biopet-bamstats is a Java program that comes with a custom wrapper shell script.
+    By default 'no default java option' is set in the wrapper.
+    The command that runs the program is 'biopet-bamstats'.
+    If you want to overwrite it you can specify memory options directly after your binaries.
+    If you have _JAVA_OPTIONS set globally this will take precedence.
+    For example run it with 'biopet-bamstats -Xms512m -Xmx1g'.
+

recipes/biopet-bamstats/biopet-bamstats.py

@@ -17,7 +17,7 @@
 from os import getenv
 from os import X_OK
 
-jar_file = 'BamStats-assembly-1.0.jar'
+jar_file = 'BamStats-assembly-1.0.1.jar'
 
 default_jvm_mem_opts = []
 

recipes/biopet-bamstats/build.sh

@@ -6,7 +6,7 @@
 outdir=$PREFIX/share/$PKG_NAME
 mkdir -p $outdir
 mkdir -p $PREFIX/bin
-cp BamStats-assembly-1.0.jar $outdir/BamStats-assembly-1.0.jar
+cp BamStats-assembly-1.0.1.jar $outdir/BamStats-assembly-1.0.1.jar
 cp $RECIPE_DIR/biopet-bamstats.py $outdir/biopet-bamstats
 ln -s $outdir/biopet-bamstats $PREFIX/bin
 

recipes/biopet-bamstats/meta.yaml

@@ -3,10 +3,10 @@
 
 package:
   name: biopet-bamstats
-  version: '1.0'
+  version: 1.0.1
 source:
-  url: https://github.com/biopet/bamstats/releases/download/v1.0/BamStats-assembly-1.0.jar
-  sha256: 5e4734aaef861779c8ce99b86b0e92e6103533f3c93fd2d22ef6bb08be26f97b
+  url: https://github.com/biopet/bamstats/releases/download/v1.0.1/BamStats-assembly-1.0.1.jar
+  sha256: ab1beffd8a5a51e2937cb5efa190d6e57fb8e63d6b19a92e8e83d7db2a9b839e
 build:
   noarch: generic
   number: 0