Add EGA-Cryptor

recipes/ega-cryptor/build.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+set -e -x
+set -eu -o pipefail
+
+outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
+mkdir -p $outdir
+ln -s $PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM $PREFIX/share/$PKG_NAME
+mkdir -p $PREFIX/bin
+cp -Rf * $outdir/
+mv $outdir/ega-cryptor-$PKG_VERSION.jar $outdir/ega-cryptor.jar
+cp -f $RECIPE_DIR/ega-cryptor.py $outdir/ega-cryptor
+ln -sf $outdir/ega-cryptor $PREFIX/bin
+chmod 0755 "${PREFIX}/bin/ega-cryptor"
+

recipes/ega-cryptor/ega-cryptor.py

@@ -0,0 +1,102 @@
+#!/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 = 'ega-cryptor-2.0.0.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()
+    """
+    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:])
+    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/ega-cryptor/meta.yaml

@@ -0,0 +1,36 @@
+{% set version = "2.0.0" %}
+
+package:
+  name: ega-cryptor
+  version: {{ version }}
+
+build:
+  noarch: generic
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('ega-cryptor', max_pin="2.0.0") }}
+
+source:
+  url: https://ega-archive.org/assets/files/EgaCryptor.zip
+  sha256: 402d9d1d5de8beea416d3e8dc8e10c3fd1e7548e4d6e29d503afe1fcbe11ff8a
+
+requirements:
+  run:
+    - openjdk >=8
+    - python
+
+test:
+  commands:
+    - ega-cryptor -h
+
+about:
+  home: https://ega-archive.org/submission/data/file-preparation/egacryptor/
+  summary: EGACryptor v.2.0.0
+  license: unknown
+  description: |
+    The EGACryptor v.2.0.0 is a JAVA-based application which enables submitters 
+    to produce EGA compliant encrypted files along with files for the encrypted
+    and unencrypted md5sum for each file to be submitted. The application will 
+    generate an output folder that will by default mirror the directory structure
+    containing the original files. This output folder can subsequently be uploaded
+    to the EGA FTP staging area via an FTP or Aspera client.