| Previous changeset 126:def0f754ee1b (2021-03-26) Next changeset 128:56aa8105000d (2021-03-30) |
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Commit message:
Uploaded |
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modified:
toolfactory/rgToolFactory2.py |
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removed:
toolfactory/testtf.sh toolfactory/whoosh.sh |
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| diff -r def0f754ee1b -r 98c8a76b3638 toolfactory/rgToolFactory2.py --- a/toolfactory/rgToolFactory2.py Fri Mar 26 09:29:58 2021 +0000 +++ b/toolfactory/rgToolFactory2.py Tue Mar 30 00:17:55 2021 +0000 |
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| @@ -27,15 +27,13 @@ import tempfile import time -from bioblend import ConnectionError -from bioblend import toolshed import galaxyxml.tool as gxt import galaxyxml.tool.parameters as gxtp - import lxml - import yaml +from bioblend import ConnectionError +from bioblend import toolshed myversion = "V2.2 February 2021" @@ -490,11 +488,11 @@ aninput.positional = self.is_positional if self.is_positional: if p["origCL"].upper() == "STDIN": - aparm.positional = 9999998 - aparm.command_line_override = "> $%s" % newname + aninput.positional = 9999998 + aninput.command_line_override = "> $%s" % newname else: - aparm.positional = int(p["origCL"]) - aparm.command_line_override = "$%s" % newname + aninput.positional = int(p["origCL"]) + aninput.command_line_override = "$%s" % newname self.tinputs.append(aninput) tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname) self.testparam.append(tparm) @@ -990,7 +988,6 @@ src = os.path.join(self.testdir, entry.name) shutil.copyfile(src, dest) - def planemo_test_once(self): """planemo is a requirement so is available for testing but needs a different call if in the biocontainer - see above |
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| diff -r def0f754ee1b -r 98c8a76b3638 toolfactory/testtf.sh --- a/toolfactory/testtf.sh Fri Mar 26 09:29:58 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -planemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/galaxy/tools/tool_makers/toolfactory &>foo - |
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| diff -r def0f754ee1b -r 98c8a76b3638 toolfactory/whoosh.sh --- a/toolfactory/whoosh.sh Fri Mar 26 09:29:58 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,16 +0,0 @@ -# using the galaxy venv this seems to work -. /galaxy_venv/bin/activate -python scripts/tool_shed/build_ts_whoosh_index.py -c config/tool_shed.yml --config-section tool_shed -# eeesh. /etc/galaxy is where the actual galaxy.yml lives - despite other configs being where they might be expected -# fix tool_shed.yml to 0.0.0.0 and admin email -# add tgz to datatypes :( -# need to source a venv in /export/tool_deps/toolfactorydeps/0.01/fubar/toolfactorydeps/9e9428fe9134/env.sh -# as nothing was done by the setup_virtualenv step apparently. -# gcc and friends for planemo pip installation -# File "/galaxy-central/lib/galaxy/tool_util/verify/interactor.py", line 595, in <listcomp> -# test_user = [user for user in all_users if user["email"] == email][0] -# add local to tool_sheds_conf.xml -# <tool_sheds> -# <tool_shed name="local" url="http://localhost:9009"/> -# mercurial > 5.5!! - |