| mkdir -p ~/src/test/test_install_dir | |
| cd ~/src/test/ | |
| wget http://www.cpan.org/authors/id/A/AP/APEIRON/local-lib-1.008009.tar.gz | |
| tar xfvz local-lib-1.008009.tar.gz | |
| cd local-lib-1.008009 | |
| export INSTALL_DIR=~/src/test/test_install_dir | |
| export HOME=$INSTALL_DIR; export PATH=$INSTALL_DIR/bin/:$PATH; perl Makefile.PL --bootstrap=$INSTALL_DIR/local-lib/ --no-manpages | |
| make install | |
| echo "test local-lib/perl5" | |
| #This should fail with Can't locate local/lib.pm in @INC |
| diff --git a/lib/galaxy/datatypes/dataproviders/dataset.py b/lib/galaxy/datatypes/dataproviders/dataset.py | |
| index 1fe1868..c34cd42 100644 | |
| --- a/lib/galaxy/datatypes/dataproviders/dataset.py | |
| +++ b/lib/galaxy/datatypes/dataproviders/dataset.py | |
| @@ -633,6 +633,7 @@ class SamtoolsDataProvider( line.RegexLineDataProvider ): | |
| command.extend( self.to_options_list( options_string, options_dict ) ) | |
| command.append( self.dataset.file_name ) | |
| command.extend( regions ) | |
| + command.extend( ['| samtools sort -']) | |
| return command |
| diff --git a/test/base/twilltestcase.py b/test/base/twilltestcase.py | |
| index bced847..e2009f5 100644 | |
| --- a/test/base/twilltestcase.py | |
| +++ b/test/base/twilltestcase.py | |
| @@ -2487,9 +2487,9 @@ class TwillTestCase( unittest.TestCase ): | |
| temp_local = tempfile.NamedTemporaryFile( suffix='.sam', prefix='local_bam_converted_to_sam_' ) | |
| fd, temp_temp = tempfile.mkstemp( suffix='.sam', prefix='history_bam_converted_to_sam_' ) | |
| os.close( fd ) | |
| - command = 'samtools view -h -o "%s" "%s"' % ( temp_local.name, local_name ) | |
| + command = 'samtools sort -o "%s" - |samtools view -h -o "%s" -' % ( local_name, temp_local.name ) |
| { | |
| "a_galaxy_workflow": "true", | |
| "annotation": "", | |
| "format-version": "0.1", | |
| "name": "ChIP-seq analysis", | |
| "steps": { | |
| "0": { | |
| "annotation": "", | |
| "id": 0, | |
| "input_connections": {}, |
| <?xml version="1.0"?> | |
| <tool_dependency> | |
| <package name="libpng" version="1.6.7"> | |
| <repository name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" /> | |
| </package> | |
| <package name="pixman" version="0.32.6"> | |
| <install version="1.0"> | |
| <actions_group> | |
| <actions architecture="x86_64" os="linux"> | |
| <action type="download_by_url" sha256sum="3dfed13b8060eadabf0a4945c7045b7793cc7e3e910e748a8bb0f0dc3e794904">http://cairographics.org/releases/pixman-0.32.6.tar.gz</action> |
| <!DOCTYPE html> | |
| <html lang="en"> | |
| <head> | |
| <meta charset="utf-8"> | |
| <meta http-equiv="X-UA-Compatible" content="IE=edge"> | |
| <meta name="viewport" content="width=device-width, initial-scale=1"> | |
| <title>Tool Test Results (powered by Planemo)</title> | |
| <!-- Bootstrap --> | |
| <style>/*! |
Ubuntu-14.04 LTS container in LXC container:
Activate trusty-backports in /etc/apt/sources.list.d/trusty-backports
deb http://fr.archive.ubuntu.com/ubuntu/ trusty-backports main restricted universe multiverse
deb-src http://fr.archive.ubuntu.com/ubuntu/ trusty-backports main restricted universe multiverse
| diff --git a/fc-cache/fc-cache.c b/fc-cache/fc-cache.c | |
| index 99e0e9f..bf3b6b4 100644 | |
| --- a/fc-cache/fc-cache.c | |
| +++ b/fc-cache/fc-cache.c | |
| @@ -187,13 +187,8 @@ scanDirs (FcStrList *list, FcConfig *config, FcBool force, FcBool really_force, | |
| if (!cache) | |
| { | |
| - if (!recursive) | |
| - cache = FcDirCacheRescan (dir, config); |
| #!/bin/bash | |
| # This script is run by Supervisor to start PostgreSQL 9.1 in foreground mode | |
| function shutdown() | |
| { | |
| echo "Shutting down PostgreSQL" | |
| kill $(cat /var/lib/postgresql/9.3/main/postmaster.pid) | |
| exit 0 | |
| } |
| #!/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 |