pjbriggs

#!/usr/bin/env perl
#
# Client JSV script from Mark Lundie for running cellranger
# pipeline
#
# Strips "-pe smp.pe 1" lines from job submission scripts
# (requests for >1 core will be kept unchanged)
#
# Include in qsub commands using -jsv PATH/TO/sge.strip_pe.pl

pjbriggs

#!/bin/bash
#
# Run example CRAFT-GP pipeline based on docs
#
# 0. Set up test data
if [ ! -d test-data ] ; then
    mkdir test-data
fi
cat >test-data/test_index_snps.in <<EOF
rs	chr	position

pjbriggs

#!/usr/bin/bash
#
packages="dplyr coloc readr tidyr stringr optparse"

export INSTALL_DIR=$(pwd)/R_LIBS/CRAFT-GP
if [ ! -d $INSTALL_DIR ] ; then
    mkdir -p $INSTALL_DIR
fi
export R_LIBS=$R_LIBS:$INSTALL_DIR
for package in $packages ; do

pjbriggs

diff --git a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
index 3d28462..5c98da6 100755
--- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
@@ -81,7 +81,7 @@ class CompressedFile( object ):
         if self.file_type == 'zip':
             for zipped_file in self.getmembers():
                 filename = self.getname( zipped_file )
-                absolute_filepath = os.path.join( extraction_path, filename )
+                absolute_filepath = os.path.join( path, filename )

pjbriggs

#!/bin/bash -e
#
# Migrate "legacy" config files in Galaxy distribution
#
# Check nothing is running
if [ ! -z "$(ls *.pid 2>/dev/null)" ] ; then
   echo ERROR check you have stopped all Galaxy processes >&2
   exit 1
fi
#

pjbriggs

#!/bin/sh
#
# Generate test outputs for clustering
#
# Existing test case (--cluster_fast)
vsearch  \
    --notrunclabels \
    --cluster_fast BioMarKs5k.fsa.bz2 \
    --maxrejects 2 \
    --maxaccepts 1 \

pjbriggs

#!/usr/bin/env python
#
# Convert bedgraph file into wig format
#
# Based on perl script by Dave Tang
# http://davetang.org/wiki/tiki-index.php?page=wig
import optparse
import os
import gzip

pjbriggs

#!/usr/bin/env python
#
# Make generic CEAS annotation file for arbitrary genome build
#
# Needs the UCSC fetchChromSizes program plus build_genomeBG from CEAS
#
# Usage: make_ceas_refseq_annotation.py <GENOME>
#
import optparse
import os

pjbriggs

diff -r c3cef260df88 lib/galaxy/webapps/galaxy/controllers/history.py
--- a/lib/galaxy/webapps/galaxy/controllers/history.py	Fri May 15 15:20:17 2015 -0400
+++ b/lib/galaxy/webapps/galaxy/controllers/history.py	Wed Jun 17 12:51:41 2015 +0100
@@ -899,7 +899,7 @@
         for history_id in ids:
             history_id = self.decode_id( history_id )
             history = self.history_manager.get_owned( history_id, trans.user, current_history=trans.history )
-            histories.append(  )
+            histories.append( history )
         return histories

pjbriggs

       ...
        location ^~ /reports/ {
            proxy_pass  http://reports;
            proxy_set_header   X-Forwarded-Host $host;
            proxy_set_header   X-Forwarded-For  $proxy_add_x_forwarded_for;
            auth_basic "Restricted";
            auth_basic_user_file /etc/nginx/galaxy-reports.htpasswd;
        ...
	}