Add EGA-Cryptor

recipes/ega-cryptor/build.sh

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+#!/usr/bin/env 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/ega-cryptor-$PKG_VERSION.jar $outdir/ega-cryptor.jar
+cp -f $RECIPE_DIR/ega-cryptor.py $outdir/ega-cryptor
+chmod +x $outdir/ega-cryptor
+ln -sf $outdir/ega-cryptor $PREFIX/bin

recipes/ega-cryptor/ega-cryptor.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 = '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') or 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 explicitly 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 does 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])
+
+ jar_arg = '-cp' if pass_args and pass_args[0].startswith('eu') else '-jar'
+
+ jar_path = os.path.join(jar_dir, jar_file)
+
+ java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args
+
+ return_code = subprocess.call(java_args)
+ if return_code != 0:
+ sys.stderr.write(f"Java process exited with return code {return_code}\n")
+ sys.exit(return_code)
+
+if __name__ == '__main__':
+ main()

recipes/ega-cryptor/meta.yaml

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+{% set version = "2.0.0" %}
+
+package:
+ name: ega-cryptor
+ version: {{ version }}
+
+build:
+ noarch: generic
+ number: 0
+ run_exports:
+ - {{ pin_compatible('ega-cryptor', max_pin="x.x.x") }}
+
+source:
+ url: https://ega-archive.org/assets/files/EgaCryptor.zip
+ sha256: 402d9d1d5de8beea416d3e8dc8e10c3fd1e7548e4d6e29d503afe1fcbe11ff8a
+
+requirements:
+ build:
+ - unzip
+ run:
+ - openjdk >=8
+ - python >=3.6
+
+test:
+ commands:
+ - "ega-cryptor -h"
+
+about:
+ home: https://ega-archive.org/submission/data/file-preparation/egacryptor/
+ summary: EGACryptor v.2.0.0
+ license: Apache-2.0
+ 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. 
+# Description extracted from the EGA-Cryptor website.