diff autogenJB2.py @ 53:bdfa6a7c4543 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4-dirty

--- a/autogenJB2.py	Thu Mar 07 06:41:01 2024 +0000
+++ b/autogenJB2.py	Thu Mar 07 09:23:06 2024 +0000
@@ -129,10 +129,8 @@
                 elif trext == "cram":
                     ipath  = track[3]
                     if not os.path.exists(ipath):
-                        jc.logging.info('calling %s' % ' '.join(cmd))
                         ipath = os.path.realpath(os.path.join('./', trackname + '.crai'))
                         cmd = ["samtools", "index", "-c", "-o", ipath, os.path.realpath(track[0])]
-                        sys.stdout.write('#### calling %s' % ' '.join(cmd))
                         jc.subprocess_check_call(cmd)
                     track_conf.update({"conf": {"options": {"cram": {"cram_index": ipath}}}})
                 track_conf["path"] = tpath