JBrowse2: Revert from pif indexes for paf (#1522)

* 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.

* problem with pif
revert to paf until sorted

* return to using paf unindexed until figure out why the jbrowse utility is broken
tabix does not do this.

* remove tabix code - won't work.

* remove debug ls

* flake8

tools/jbrowse2/jbrowse2.py

@@ -1130,18 +1130,24 @@ def add_bed(self, data, ext, trackData):
         self.trackIdlist.append(tId)
 
     def add_paf(self, data, trackData, pafOpts, **kwargs):
+        canPIF = False
         tname = trackData["name"]
         tId = trackData["label"]
         url = tId
-        usePIF = False  # much faster if indexed remotely or locally
+        usePIF = False  # much faster if indexed remotely or locally but broken in biocontainer.
         useuri = data.startswith("http://") or data.startswith("https://")
         if not useuri:
-            url = "%s.pif.gz" % tId
-            cmd = "sort -b -k1,1 -k2,3n -k3,4n '%s' | bgzip -c > '%s'" % (data, url)
-            self.subprocess_popen(cmd)
-            cmd = ["tabix", "-b", "3", "-e", "4", "-f", url]
-            self.subprocess_check_call(cmd)
-            usePIF = True
+            if canPIF:
+                fakeName = '%s.paf' % tId
+                url = "%s.pif.gz" % tId
+                cmd = ["cp", data, fakeName]
+                self.subprocess_check_call(cmd)
+                cmd = ["jbrowse", "make-pif", fakeName]  # jbrowse pif input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also
+                self.subprocess_check_call(cmd)
+                usePIF = True
+            else:
+                dest = os.path.join(self.outdir, url)
+                self.symlink_or_copy(os.path.realpath(data), dest)
         else:
             url = data
             if data.endswith(".pif.gz") or data.endswith(".paf.gz"):  # is tabix

tools/jbrowse2/jbrowse2.xml

@@ -666,11 +666,16 @@ export JBROWSE2_PATH=\$(realpath \$(dirname \$(which jbrowse))/../opt/jbrowse2)
                     <has_archive_member path="merlinlastz.maf_6.sorted.bed.gz.tbi"/>
                     <has_archive_member path="merlin.blastxml_7.gz"/>
                     <has_archive_member path="dm3test.cool_9.hic"/>
-                    <has_archive_member path="peach-grape-map.paf_10.pif.gz"/>
-                    <has_archive_member path="peach-grape-map.paf_10.pif.gz.tbi"/>
+                    <has_archive_member path="peach-grape-map.paf_10"/>
                     <has_archive_member path="arabgrapepeach.paf_11"/>
-                    <has_archive_member path="arabgrapepeach.paf_11.pif.gz"/>
-                    <has_archive_member path="arabgrapepeach.paf_11.pif.gz.tbi"/>
+                    <has_archive_member path="Merlin.fa.gz.fai"/>
+                    <has_archive_member path="dm3.fa.fa.gz.fai"/>
+                    <has_archive_member path="Ppersica1.fa.fa.gz"/>
+                    <has_archive_member path="Ppersica1.fa.fa.gz.fai"/>
+                    <has_archive_member path="Ppersica1.fa.fa.gz.gzi"/>
+                    <has_archive_member path="Vvinifera1.fa.fa.gz.fai"/>
+                    <has_archive_member path="Vvinifera1.fa.fa.gz"/>
+                    <has_archive_member path="Vvinifera1.fa.fa.gz.gzi"/>
                     <has_archive_member path="Merlin.fa.gz.fai"/>
                     <has_archive_member path="dm3.fa.fa.gz.fai"/>
                     <has_archive_member path="Ppersica1.fa.fa.gz"/>
@@ -680,9 +685,7 @@ export JBROWSE2_PATH=\$(realpath \$(dirname \$(which jbrowse))/../opt/jbrowse2)
                     <has_archive_member path="Vvinifera1.fa.fa.gz"/>
                     <has_archive_member path="Vvinifera1.fa.fa.gz.gzi"/>
                     <has_archive_member path="config.json">
-                        <has_json_property_with_text property="type" text="PairwiseIndexedPAFAdapter"/>
-                        <has_json_property_with_text property="uri" text="peach-grape-map.paf_10.pif.gz.tbi"/>
-                        <has_json_property_with_text property="uri" text="peach-grape-map.paf_10.pif.gz"/>
+                        <has_json_property_with_text property="uri" text="Vvinifera1.fa.fa.gz.fai"/>
                     </has_archive_member>
                 </assert_contents>
             </output>

tools/jbrowse2/macros.xml

@@ -25,7 +25,7 @@
         </requirements>
     </xml>
     <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
-    <token name="@VERSION_SUFFIX@">5</token>
+    <token name="@VERSION_SUFFIX@">6</token>
     <xml name="creators">
         <creator>
             <person givenName="Helena" familyName="Rasche" url="https://github.com/hexylena"/>