Update JBrowse2 to 2.17.0 (bgruening#1553)

* 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 * Idiotic sort error generates broken pif indexes. Pity the built in fails in biocontainers. * bump to 2.17.0
planemo-autoupdate · Dec 4, 2024 · 35f23ea · 35f23ea
1 parent fb12992
commit 35f23ea
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Showing 3 changed files with 17 additions and 10 deletions.
diff --git a/tools/jbrowse2/jbrowse2.py b/tools/jbrowse2/jbrowse2.py
@@ -615,8 +615,10 @@ def write_config(self):
 
     def text_index(self):
         # Index tracks
-        args = ["jbrowse", "text-index"]
-        self.subprocess_check_call(args)
+        e = os.environ
+        e["SHELL"] = "/bin/sh"
+        cmd = ["jbrowse", "text-index"]
+        subprocess.run(cmd, env=e, shell=True)
 
     def add_hic(self, data, trackData):
         """
@@ -1108,12 +1110,14 @@ def add_paf(self, data, trackData, pafOpts, **kwargs):
                 url = "%s.pif.gz" % tId
                 cmd = ["cp", data, fakeName]
                 self.subprocess_check_call(cmd)
+                e = os.environ
+                e["SHELL"] = "/bin/sh"
                 cmd = [
                     "jbrowse",
                     "make-pif",
                     fakeName,
                 ]
-                self.subprocess_check_call(cmd)
+                subprocess.run(cmd, env=e, shell=True)
                 usePIF = True
             else:
                 dest = os.path.join(self.outdir, url)
@@ -1534,9 +1538,10 @@ def clone_jbrowse(self, realclone=False):
         """
         dest = self.outdir
         if (not os.path.exists(self.jbrowse2path)) or realclone:
-            self.subprocess_check_call(
-                ["jbrowse", "create", dest, "-f", "--tag", f"{JB2VER}"]
-            )
+            e = os.environ
+            e["SHELL"] = "/bin/sh"
+            cmd = ["jbrowse", "create", dest, "-f", "--tag", f"{JB2VER}"]
+            subprocess.run(cmd, env=e, shell=True)
         else:
             shutil.copytree(self.jbrowse2path, dest, dirs_exist_ok=True)
         for fn in [

diff --git a/tools/jbrowse2/jbrowse2.xml b/tools/jbrowse2/jbrowse2.xml
@@ -539,6 +539,7 @@ export JBROWSE2_PATH=\$(realpath \$(dirname \$(which jbrowse))/../opt/jbrowse2)
                 </conditional>
                 <repeat name="track_groups">
                     <param name="category" value="Assembly properties"/>
+
                     <repeat name="data_tracks">
                         <conditional name="data_format">
                             <param name="data_format_select" value="paf"/>
@@ -552,6 +553,7 @@ export JBROWSE2_PATH=\$(realpath \$(dirname \$(which jbrowse))/../opt/jbrowse2)
                             </conditional>
                         </conditional>
                     </repeat>
+
                     <repeat name="data_tracks">
                         <conditional name="data_format">
                             <param name="data_format_select" value="paf"/>
@@ -614,7 +616,7 @@ export JBROWSE2_PATH=\$(realpath \$(dirname \$(which jbrowse))/../opt/jbrowse2)
             </section>
             <output name="output" ftype="zip">
                 <assert_contents>
-                    <has_archive_member path=".*" n="676" delta="10"/>
+                    <has_archive_member path=".*" n="664" delta="10"/>
                     <has_archive_member path="index.html"/>
                     <has_archive_member path="manifest.json">
                         <has_text text="favicon.ico"/>
@@ -676,7 +678,7 @@ export JBROWSE2_PATH=\$(realpath \$(dirname \$(which jbrowse))/../opt/jbrowse2)
             </section>
             <output name="output" ftype="zip">
                 <assert_contents>
-                    <has_archive_member path=".*" n="652" delta="10"/>
+                    <has_archive_member path=".*" n="640" delta="10"/>
                     <has_archive_member path="index.html"/>
                     <has_archive_member path="manifest.json">
                         <has_text text="favicon.ico"/>

diff --git a/tools/jbrowse2/macros.xml b/tools/jbrowse2/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.15.4</token>
+    <token name="@TOOL_VERSION@">2.17.0</token>
     <xml name="edamInc">
         <edam_topics>
             <edam_topic>topic_3307</edam_topic>
@@ -25,7 +25,7 @@
         </requirements>
     </xml>
     <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
-    <token name="@VERSION_SUFFIX@">7</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="creators">
         <creator>
             <person givenName="Helena" familyName="Rasche" url="https://github.com/hexylena"/>