Mercurial > repos > fubar > jbrowse2
changeset 39:bc57164eb270 draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit ace841acd53be99494ed9bba8bb9e2ae212d3661
| author | fubar |
|---|---|
| date | Fri, 01 Mar 2024 01:03:09 +0000 |
| parents | 07849bf248e3 |
| children | e1a3d3221ed3 |
| files | __pycache__/jbrowse2.cpython-310.pyc autogenJB2.py autogenJB2.xml |
| diffstat | 3 files changed, 5 insertions(+), 2 deletions(-) [+] |
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--- a/autogenJB2.py Fri Mar 01 00:40:38 2024 +0000 +++ b/autogenJB2.py Fri Mar 01 01:03:09 2024 +0000 @@ -43,9 +43,9 @@ default=[], action="append", ) - + parser.add_argument("--jbrowse2path", help="Path to JBrowse2 directory in biocontainer or Conda") + parser.add_argument("--outdir", help="Output directory", required=True) parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.10.2") - parser.add_argument("--outdir", help="Output directory", required=True) args = parser.parse_args() sessName = args.sessName # --trackmeta $jbrowseme[$key],$jbrowseme[$key].ext,'$key' @@ -63,6 +63,7 @@ genome_names = [x[2] for x in listgenomes] jc = jbC( outdir=args.outdir, + jbrowse2path=args.jbrowse2path, genomes=[ { "path": x,
--- a/autogenJB2.xml Fri Mar 01 00:40:38 2024 +0000 +++ b/autogenJB2.xml Fri Mar 01 01:03:09 2024 +0000 @@ -10,6 +10,7 @@ <expand macro="requirements"/> <version_command>python '${__tool_directory__}/autogenJB2.py' --version</version_command> <command detect_errors="aggressive"><![CDATA[ +export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 && python '$__tool_directory__/autogenJB2.py' #for $key in $autoCollection.keys(): #if $autoCollection[$key].ext == 'fasta': @@ -23,6 +24,7 @@ #end if #end for --outdir '$output.files_path' +--jbrowse2path \${JBROWSE2_PATH} --sessName "Autogen JBrowse" && cp '$output.files_path/index.html' '$output'