Mercurial > repos > peterjc > effectivet3

comparison tools/effectiveT3/effectiveT3.py @ 25:69ba0f4e91af draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit 5fb6ee31f33e8e24c1ae5d56c93ac3e0157dad72-dirty
author peterjc
date Thu, 09 Feb 2017 11:20:53 -0500
parents a3d660e900b1
children af14f755c05b
comparison
equal deleted inserted replaced
24:a3d660e900b1 25:69ba0f4e91af
9 9
10 It then calls the standalone Effective T3 v1.0.1 program (not the 10 It then calls the standalone Effective T3 v1.0.1 program (not the
11 webservice), and reformats the semi-colon separated output into 11 webservice), and reformats the semi-colon separated output into
12 tab separated output for use in Galaxy. 12 tab separated output for use in Galaxy.
13 """ 13 """
14 import sys
15 import os 14 import os
16 import subprocess 15 import subprocess
16 import sys
17 17
18 # The Galaxy auto-install via tool_dependencies.xml will set this environment variable 18 # The Galaxy auto-install via tool_dependencies.xml will set this environment variable
19 effective_t3_dir = os.environ.get("EFFECTIVET3", "/opt/EffectiveT3/") 19 effective_t3_dir = os.environ.get("EFFECTIVET3", "/opt/EffectiveT3/")
20 effective_t3_jar = os.path.join(effective_t3_dir, "TTSS_GUI-1.0.1.jar") 20 effective_t3_jar = os.path.join(effective_t3_dir, "TTSS_GUI-1.0.1.jar")
21 21