Add recipe for SNVer 0.5.3

recipes/snver/SNVerIndividual.py

@@ -0,0 +1,97 @@
+#!/usr/bin/env python
+#
+# Wrapper script for Java Conda packages that ensures that the java runtime
+# is invoked with the right options. Adapted from the bash script (http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128).
+
+#
+# Program Parameters
+#
+import os
+import subprocess
+import sys
+import shutil
+from os import access
+from os import getenv
+from os import X_OK
+jar_file = 'SNVerIndividual.jar'
+
+
+default_jvm_mem_opts = ['-Xms512m', '-Xmx1g']
+
+# !!! 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():
+    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/snver/SNVerPool.py

@@ -0,0 +1,97 @@
+#!/usr/bin/env python
+#
+# Wrapper script for Java Conda packages that ensures that the java runtime
+# is invoked with the right options. Adapted from the bash script (http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128).
+
+#
+# Program Parameters
+#
+import os
+import subprocess
+import sys
+import shutil
+from os import access
+from os import getenv
+from os import X_OK
+jar_file = 'SNVerPool.jar'
+
+
+default_jvm_mem_opts = ['-Xms512m', '-Xmx1g']
+
+# !!! 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():
+    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/snver/build.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+set -eu -o pipefail
+
+outdir=$PREFIX/opt/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
+mkdir -p $outdir
+mkdir -p $PREFIX/bin
+cp -R * $outdir/
+cp $RECIPE_DIR/SNVerIndividual.py $outdir/SNVerIndividual.py
+cp $RECIPE_DIR/SNVerPool.py $outdir/SNVerPool.py
+ln -s $outdir/SNVerIndividual.py $PREFIX/bin/snver
+ln -s $outdir/SNVerPool.py $PREFIX/bin/snver-pool
+chmod 0755 "${PREFIX}/bin/snver"
+chmod 0755 "${PREFIX}/bin/snver-pool"

recipes/snver/meta.yaml

@@ -0,0 +1,43 @@
+{% set name = "snver" %}
+{% set version = "0.5.3" %}
+
+about:
+  home: http://snver.sourceforge.net/
+  license: GNU General Public License version 3.0 (GPLv3)
+  summary: |
+    SNVer is a statistical tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data.
+    It reports one single overall p-value for evaluating the significance of a candidate locus being a variant, based on which multiplicity control can be obtained.
+    Loci with any (low) coverage can be tested and depth of coverage will be quantitatively factored into final significance calculation.
+    SNVer runs very fast, making it feasible for analysis of whole-exome sequencing data, or even whole-genome sequencing data. 
+
+package:
+  name: snver
+  version: {{ version }}
+
+build:
+  noarch: generic
+  number: 0
+
+source:
+  url: https://sourceforge.net/projects/snver/files/SNVer-{{ version }}.tar.gz
+  sha256: ac387873370941ab1b379def51252f40e819b0529e06f8cd8f04b61fea1b6cf8
+
+requirements:
+  host:
+  run:
+    - openjdk >=6
+    - python
+
+test:
+  commands:
+    - snver
+    - snver-pool
+
+extra:
+  notes: |
+    SNVer is Java program that comes with a custom wrapper shell script.
+    This shell wrapper is called "opsin" and is on $PATH by default. By default
+    "-Xms512m -Xmx1g" is set in the wrapper. If you want to overwrite it you can
+    specify these values directly after your binaries. If you have _JAVA_OPTIONS
+    set globally this will take precedence.
+    For example run it with "snver -Xms512m -Xmx1g"