Mercurial > repos > fubar > jbrowse2

diff jbrowse2.py @ 118:794aecef8327 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7b6920fd88a86cdb48dc4af2c6be77161eb85699-dirty
author fubar
date Sat, 21 Sep 2024 04:01:38 +0000
parents 56f9a6e0fe80
children af482048ca1a
line wrap: on
line diff
--- a/jbrowse2.py	Mon Sep 02 09:56:39 2024 +0000
+++ b/jbrowse2.py	Sat Sep 21 04:01:38 2024 +0000
@@ -411,7 +411,7 @@
             []
         )  # for default session - these are read as first line of the assembly .fai
         self.giURL = GALAXY_INFRASTRUCTURE_URL
-        self.outdir = outdir
+        self.outdir = os.path.abspath(outdir)
         self.jbrowse2path = jbrowse2path
         os.makedirs(self.outdir, exist_ok=True)
         self.genome_names = []
@@ -444,7 +444,7 @@
             log.debug(command)
         p = subprocess.Popen(
             command,
-            cwd=self.get_cwd(cwd),
+            cwd=self.outdir,
             shell=True,
             stdin=subprocess.PIPE,
             stdout=subprocess.PIPE,
@@ -1440,8 +1440,6 @@
                 )
             session_views.append(view_json)
         session_name = default_data.get("session_name", "New session")
-        for key, value in mapped_chars.items():
-            session_name = session_name.replace(value, key)
         session_json["name"] = session_name
 
         if "views" not in session_json: