mvdbeek

#!/bin/sh

# Check if this is the initial commit
if git rev-parse --verify HEAD >/dev/null 2>&1
then
    echo "pre-commit: About to create a new commit..."
    against=HEAD
else
    echo "pre-commit: About to create the first commit..."
    against=4b825dc642cb6eb9a060e54bf8d69288fbee4904

mvdbeek

#!/usr/bin/env bash
# clone a number of forks into DIR.
# never touch them. To keep things synchronized,
# call this script with the directories holding the clones
# upload_repos.sh path_to_repo_dirs/

function update_repos {

    # Author : Hemanth.HM
    # License : MIT

mvdbeek

brew install jq
curl --silent https://mississippi.snv.jussieu.fr/workflow/export_to_file?id=72f7664cb8ff9a95| jq 

mvdbeek

{
    "a_galaxy_workflow": "true", 
    "annotation": "", 
    "format-version": "0.1", 
    "name": "metavisitor PLoS-NTD - With hg38 subtraction", 
    "steps": {
        "0": {
            "annotation": "", 
            "content_id": null, 
            "id": 0, 

mvdbeek

{
    "a_galaxy_workflow": "true", 
    "annotation": "", 
    "format-version": "0.1", 
    "name": "metavisitor PLoS-NTD - With hg38 subtraction", 
    "steps": {
        "0": {
            "annotation": "", 
            "id": 0, 
            "input_connections": {}, 

mvdbeek

HTTPError: HTTP Error 500: Internal Server Error
  File "galaxy/web/framework/middleware/sentry.py", line 32, in __call__
    iterable = self.application(environ, start_response)
  File "home/galaxy/galaxy-dist/.venv/local/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__
    return self.application(environ, start_response)
  File "home/galaxy/galaxy-dist/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__
    return self.application(environ, start_response)
  File "galaxy/web/framework/base.py", line 126, in __call__
    return self.handle_request( environ, start_response )
  File "galaxy/web/framework/base.py", line 184, in handle_request

mvdbeek

(.clean_venv)marius@mississippi:~/src$ python --version
Python 2.7.6
(.clean_venv)marius@mississippi:~/src$ git clone --depth=50 https://github.com/galaxyproject/galaxy
Cloning into 'galaxy'...
remote: Counting objects: 38994, done.
remote: Compressing objects: 100% (15733/15733), done.
remote: Total 38994 (delta 27732), reused 32654 (delta 22856), pack-reused 0
Receiving objects: 100% (38994/38994), 42.99 MiB | 305.00 KiB/s, done.
Resolving deltas: 100% (27732/27732), done.
Checking connectivity... done.

mvdbeek

#############################################
PATH=/home/galaxy/tool_dependency/perl/5.18.1/iuc/package_perl_5_18/8b3509930a44/bin:$PATH; export PATH
PERL5LIB=/home/galaxy/tool_dependency/perl/5.18.1/iuc/package_perl_5_18/8b3509930a44/lib/perl5:$PERL5LIB; export PERL5LIB
PERL_ROOT_DIR=/home/galaxy/tool_dependency/perl/5.18.1/iuc/package_perl_5_18/8b3509930a44; export PERL_ROOT_DIR
PERL_LOCALLIB_DIR=/home/galaxy/tool_dependency/perl/5.18.1/iuc/package_perl_5_18/8b3509930a44/local-lib; export PERL_LOCALLIB_DIR
PKG_CONFIG_PATH=/home/galaxy/tool_dependency/libmagic/5.25/iuc/package_libmagic_5_25/21b08f55a6ac/lib/pkgconfig:$PKG_CONFIG_PATH; export PKG_CONFIG_PATH
LD_LIBRARY_PATH=/home/galaxy/tool_dependency/libmagic/5.25/iuc/package_libmagic_5_25/21b08f55a6ac/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH
C_INCLUDE_PATH=/home/galaxy/tool_dependency/libmagic/5.25/iuc/package_libmagic_5_25/21b08f55a6ac/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH
CPLUS_INCLUDE_PATH=/home/galaxy/tool_dependency/libmagic/5.25/iuc/pac

mvdbeek

[{u'deleted': False,
  u'deprecated': False,
  u'description': u'generates readmaps and size histograms from small RNA bowtie alignments',
  u'homepage_url': u'http://artbio.fr',
  u'id': u'd6fe772f95e0378d',
  u'long_description': u'generates readmaps and size histograms from small RNA bowtie alignments. This tool belongs to the mississippi tool suite.\n',
  u'model_class': u'Repository',
  u'name': u'msp_sr_readmap_and_size_histograms',
  u'owner': u'drosofff',
  u'private': False,

mvdbeek

(.venv)mariuss-MBP:fix_numpy marius$ diff -Nru numpy-1.9.2/setup.py setup.py
--- numpy-1.9.2/setup.py	2016-03-07 12:40:02.000000000 +0100
+++ setup.py	2016-08-10 11:37:47.000000000 +0200
@@ -204,9 +204,9 @@
             site_cfg.write("[atlas]\n"
                            "library_dirs = %s\n"
                            "include_dirs = %s\n"
-                           % (os.environ['ATLAS_LIB_DIR'],
-                              os.environ['ATLAS_INCLUDE_DIR']))
-    except Exception,ex: