Commit 56d8dee8 authored by Till Bald's avatar Till Bald

initial commit

parents

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cache/
*.pyc
*~
__pycache__
dist
build
[submodule "include/cli-tools-atlas"]
path = include/cli-tools-atlas
url = git://github.com/specht/cli-tools-atlas.git
[submodule "include/proteomics-knowledge-base"]
path = include/proteomics-knowledge-base
url = git://github.com/specht/proteomics-knowledge-base.git
This diff is collapsed.
# -*- mode: python -*-
block_cipher = None
a = Analysis(['crosslink-identify-peptides.py'],
pathex=['/home/till/programming/proteomatic-scripts-hippler/include/python/',
'/home/till/programming/proteomatic-scripts-hippler/include/python/pymzml/',
'/home/till/programming/proteomatic-scripts-hippler',
'./include/python/'],
binaries=None,
datas=None,
hiddenimports=["tempfile", "json", "subprocess", "mpmath", "xml.etree.cElementTree"],
hookspath=[],
runtime_hooks=[],
excludes=[],
win_no_prefer_redirects=False,
win_private_assemblies=False,
cipher=block_cipher)
##### include mydir in distribution #######
def extra_datas(mydir):
def rec_glob(p, files):
import os
import glob
for d in glob.glob(p):
if os.path.isfile(d):
files.append(d)
rec_glob("%s/*" % d, files)
files = []
rec_glob("%s/*" % mydir, files)
extra_datas = []
for f in files:
extra_datas.append((f, f, 'DATA'))
return extra_datas
###########################################
# append the 'data' dir
a.datas += extra_datas('include')
a.datas += extra_datas('helper')
pyz = PYZ(a.pure, a.zipped_data,
cipher=block_cipher)
exe = EXE(pyz,
a.scripts,
exclude_binaries=True,
name='crosslink-identify-peptides',
debug=False,
strip=False,
upx=True,
console=True )
coll = COLLECT(exe,
a.binaries,
a.zipfiles,
a.datas,
strip=False,
upx=True,
name='crosslink-identify-peptides')
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7-Zip Command line version
~~~~~~~~~~~~~~~~~~~~~~~~~~
License for use and distribution
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
7-Zip Copyright (C) 1999-2007 Igor Pavlov.
7za.exe is distributed under the GNU LGPL + AES code license
The GNU LGPL + AES code license means that you must follow both GNU LGPL rules
and AES code license rules.
Notes:
You can use 7-Zip on any computer, including a computer in a commercial
organization. You don't need to register or pay for 7-Zip.
GNU LGPL information
--------------------
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
AES code license
----------------
Copyright (c) 2001, Dr Brian Gladman
LICENSE TERMS
The free distribution and use of this software in both source and binary
form is allowed (with or without changes) provided that:
1. distributions of this source code include the above copyright
notice, this list of conditions and the following disclaimer;
2. distributions in binary form include the above copyright
notice, this list of conditions and the following disclaimer
in the documentation and/or other associated materials;
3. the copyright holder's name is not used to endorse products
built using this software without specific written permission.
DISCLAIMER
This software is provided 'as is' with no explicit or implied warranties
in respect of its properties, including, but not limited to, correctness
and fitness for purpose.
7-Zip Command line version 4.57
-------------------------------
7-Zip is a file archiver with high compression ratio.
7za.exe is a standalone command line version of 7-Zip.
7-Zip Copyright (C) 1999-2007 Igor Pavlov.
Features of 7za.exe:
- High compression ratio in new 7z format
- Supported formats:
- Packing / unpacking: 7z, ZIP, GZIP, BZIP2 and TAR
- Unpacking only: Z
- Highest compression ratio for ZIP and GZIP formats.
- Fast compression and decompression
- Strong AES-256 encryption in 7z and ZIP formats.
7za.exe is a free software distributed under the GNU LGPL + BSD LICENSE for AES part.
Read license.txt for more information.
Source code of 7za.exe and 7-Zip can be found at
http://www.7-zip.org/
7za.exe can work in Windows 95/98/ME/NT/2000/XP/2003/Vista.
There is also port of 7za.exe for POSIX systems like Unix (Linux, Solaris, OpenBSD,
FreeBSD, Cygwin, AIX, ...), MacOS X and BeOS:
http://p7zip.sourceforge.net/
This distributive packet contains the following files:
7za.exe - 7-Zip standalone command line version.
readme.txt - This file.
copying.txt - GNU LGPL license.
license.txt - License information.
7-zip.chm - User's Manual in HTML Help format.
---
End of document
require './include/ruby/proteomatic'
require 'yaml'
# This is the hub to any other scripting language. Call with
# [path to control file]
if ARGV.empty?
puts "Usage: ruby any-language-hub.rb [control file]"
exit(1)
end
controlFilePath = ARGV.shift
object = ProteomaticScript.new(nil, false, controlFilePath)
require 'fileutils'
# GO TO THE CORRECT DIRECTORY, NO MATTER WHAT!
Dir::chdir(File::join(Dir::pwd, File::dirname($0), '..'))
require 'yaml'
require './include/ruby/proteomatic'
require './include/ruby/externaltools'
if ARGV.include?('--extToolsPath')
ExternalTools::setExtToolsPath(ARGV[ARGV.index('--extToolsPath') + 1])
end
#extensions = ['.rb', '.php', '.py', '.pl']
extensions = ['.rb', '.py', '.php']