| Previous changeset 121:478ee3e780de (2024-10-03) Next changeset 123:160f33c6ba85 (2024-10-04) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a9124072bc71dd670ee58ff8e4846e14d6d603ec |
|
modified:
__pycache__/jbrowse2.cpython-312.pyc jbrowse2.py jbrowse2.xml macros.xml |
| b |
| diff -r 478ee3e780de -r ae07c55ab96b __pycache__/jbrowse2.cpython-312.pyc |
| b |
| Binary file __pycache__/jbrowse2.cpython-312.pyc has changed |
| b |
| diff -r 478ee3e780de -r ae07c55ab96b jbrowse2.py --- a/jbrowse2.py Thu Oct 03 06:07:18 2024 +0000 +++ b/jbrowse2.py Fri Oct 04 04:07:03 2024 +0000 |
| [ |
| @@ -21,7 +21,7 @@ logging.basicConfig(level=logging.DEBUG) log = logging.getLogger("jbrowse") -JB2VER = "v2.12.3" +JB2VER = "v2.15.4" # version pinned if cloning - but not cloning now logCommands = True # useful for seeing what's being written but not for production setups @@ -1547,7 +1547,7 @@ """ dest = self.outdir - if realclone: + if (not os.path.exists(self.jbrowse2path)) or realclone: self.subprocess_check_call( ["jbrowse", "create", dest, "-f", "--tag", f"{JB2VER}"] ) |
| b |
| diff -r 478ee3e780de -r ae07c55ab96b jbrowse2.xml --- a/jbrowse2.xml Thu Oct 03 06:07:18 2024 +0000 +++ b/jbrowse2.xml Fri Oct 04 04:07:03 2024 +0000 |
| [ |
| @@ -21,7 +21,7 @@ <command detect_errors="aggressive"><![CDATA[ mkdir -p '$output.files_path' && cp '$trackxml' '$output.files_path/galaxy.xml' && -export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 && +export JBROWSE2_PATH=\$(realpath \$(dirname \$(which jbrowse))/../opt/jbrowse2) && #if $jbgen.ucol.formcoll=="collect": python '$__tool_directory__/autogenJB2.py' #for $key in $autoCollection.keys(): |
| b |
| diff -r 478ee3e780de -r ae07c55ab96b macros.xml --- a/macros.xml Thu Oct 03 06:07:18 2024 +0000 +++ b/macros.xml Fri Oct 04 04:07:03 2024 +0000 |
| b |
| @@ -25,7 +25,7 @@ </requirements> </xml> <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">3</token> <xml name="creators"> <creator> <person givenName="Helena" familyName="Rasche" url="https://github.com/hexylena"/> |