update jbrowse2 to 2.13.0 (#1465)

* adding first tested and working generated tool from https://github.com/fubar2/nftoolmaker It actually does work. Sort of. Hope this is useful to someone. * fixes suggested by bgruening for the PR - all adjustments will now apply to all future generated tools :) * add yara mapper ToolFactory - NOT from nf-core. Allows single ended fastq or fasta to be mapped, or a pair of forward and reverse - both must be fastq * small test files still work :) * single quotes for $runme - disappeared mysteriously :( * adding panaroo * Finally fixed the '$runme' suggestion and got the sanitisers not to. * fix profile="22.05" - need to update galaxyxml to fix this and the stdio replacement... * cleanup master branch of fork * update help some prompts add bgperpx - todo add as a parameter * 2.12.2 update Add wiggle track colour and other controls Add bpPerPx in advanced section to control view scale at default open Clarify dependence on remote URI tabix data if uri source used. * bump to 2.12.3 jb2 still passes tests - no breakage yet. * fix JB2VER although not currently used... * Have the no-build plugin for bed colour above and below zero binary working! Involved a substantial simplification of the default_session setup - just needed "configuration": displayId in the display. Simples. * remove copy for strings. * Update tools/jbrowse2/jbrowse2.xml Co-authored-by: Björn Grüning <[email protected]> * Update tools/jbrowse2/jbrowse2.xml Co-authored-by: Björn Grüning <[email protected]> * fix flake errors and some suggestions * thought I'd got this one... * add the new plugin js * change bed default to not use plugin * add help explaining relationship to the Bigwig extremes to bed features tool and to the advanced control form. * update to 2.13.0 release fix biotools jbrowse entry informative error message if collection has no fasta reference * decrement version suffix back to zero * remove flakery spaces --------- Co-authored-by: Björn Grüning <[email protected]>
bgruening · Jul 28, 2024 · 45375b6 · 45375b6
1 parent d4e8bcb
commit 45375b6
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Showing 3 changed files with 8 additions and 3 deletions.
diff --git a/tools/jbrowse2/autogenJB2.py b/tools/jbrowse2/autogenJB2.py
@@ -92,6 +92,11 @@
             # foo.paf must have a foo_paf.fasta or fasta.gz to match
             tnames = [x[2] for x in listtracks]
             texts = [x[1] for x in listtracks]
+            if len(listtracks) == 0:
+                sys.stderr.write(
+                    "Please add at least one track (bam,bed,bigwig,blastxml,cram,gff,hic,maf,paf or vcf) to the collection. No suitable track files for autogenJB2 - nothing to process"
+                )
+                sys.exit(5)
             for i, track in enumerate(listtracks):
                 track_conf = {
                     "trackfiles": [],
@@ -224,5 +229,5 @@
             # jc.text_index() not sure what broke here.
     else:
         sys.stderr.write(
-            "Collection has no suitable trackfiles for autogenJB2 - nothing to process"
+            "Please add a fasta genome reference to the collection. No suitable reference fasta for autogenJB2 - nothing to process"
         )
diff --git a/tools/jbrowse2/jbrowse2.xml b/tools/jbrowse2/jbrowse2.xml
@@ -5,7 +5,7 @@
     </macros>
     <expand macro="edamInc"/>
     <xrefs>
-        <xref type="bio.tools">jbrowse2</xref>
+        <xref type="bio.tools">jbrowse_2</xref>
     </xrefs>
     <expand macro="requirements"/>
     <required_files>

diff --git a/tools/jbrowse2/macros.xml b/tools/jbrowse2/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.12.3</token>
+    <token name="@TOOL_VERSION@">2.13.0</token>
     <xml name="edamInc">
         <edam_topics>
             <edam_topic>topic_3307</edam_topic>