Add hap-ibd

recipes/hap-ibd/build.sh

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+#!/bin/bash
+
+set -eu -o pipefail
+
+export LD_LIBRARY_PATH="${PREFIX}/lib"
+
+outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
+mkdir -p $outdir
+mkdir -p $PREFIX/bin
+
+cp hap-ibd.jar $outdir/hap-ibd.jar
+cp $RECIPE_DIR/hap-ibd.py $outdir/hap-ibd
+
+ln -s $outdir/hap-ibd $PREFIX/bin
+chmod 0755 "${PREFIX}/bin/hap-ibd"

recipes/hap-ibd/hap-ibd.py

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+#!/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 = 'hap-ibd.jar'
+
+
+default_jvm_mem_opts = ['-Xms2g', '-Xmx4g']
+
+# !!! 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 def_temp_log_opts(args):
+    """
+    Establish default temporary and log folders.
+    """
+    TEMP  = os.getenv("TEMP")
+
+    if TEMP is not None:
+        if '-log' not in args:
+            args.append('-log')
+            args.append(TEMP+'/logs')
+
+        if '-temp_folder' not in args :
+            args.append('-temp_folder')
+            args.append(TEMP)
+
+    return args
+
+
+def main():
+    java = java_executable()
+    """
+    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.
+    """
+    (mem_opts, prop_opts, pass_args, exec_dir) = jvm_opts(sys.argv[1:])
+    pass_args = def_temp_log_opts(pass_args)
+    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/hap-ibd/meta.yaml

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+{% set name = "hap-ibd" %}
+{% set version = "1.0.rev20May22.818" %}
+{% set sha256 = "d140accd58e9dbf5402ba66b691074ff858b454f8a1d4f2dc4ccd1ee23730e49" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://faculty.washington.edu/browning/hap-ibd.jar
+  sha256: {{ sha256 }}
+
+build:
+  number: 0
+  noarch: generic
+
+requirements:
+  run:
+    - openjdk >=8
+    - python
+
+test:
+  commands:
+    - "hap-ibd"
+
+about:
+  home: https://github.com/browning-lab/hap-ibd
+  license: Apache-2.0
+  summary: "Hap-ibd Detects identity-by-descent (IBD) segments and homozygosity-by-descent (HBD) segments in phased genotype data."
+  doc_url: https://github.com/browning-lab/hap-ibd/blob/master/README.md
+
+extra:
+  identifiers:
+    - biotools:hap-ibd
+    - doi:10.1016/j.ajhg.2020.02.010