Mercurial > repos > fubar > tool_factory_2

changeset 72:a8764cda9dbf draft

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Uploaded
author fubar
date Sat, 14 Nov 2020 08:04:59 +0000
parents eea262faed9c
children 95adf7148d9a
files toolfactory/rgToolFactory2.py toolfactory/rgToolFactory2.xml
diffstat 2 files changed, 8 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/toolfactory/rgToolFactory2.py	Sat Nov 14 06:16:34 2020 +0000
+++ b/toolfactory/rgToolFactory2.py	Sat Nov 14 08:04:59 2020 +0000
@@ -762,6 +762,7 @@
         cat = 'ToolFactory generated tools'
         if self.args.tool_name not in rnames:
             cll = ["planemo", "shed_create", "--shed_target", "local",
+            "--directory", self.args.tool_dir,
             "--owner","fubar","--name",
             self.args.tool_name,"--shed_key",
             self.args.toolshed_api_key,]
@@ -788,6 +789,7 @@
             self.args.toolshed_api_key,
             "--tar",
             self.newtarpath,
+            "--directory", self.args.tool_dir,
         ]
         p = subprocess.run(cll, shell=False, stdout=tout, stderr=tout)
         tout.write("Ran %s got %d" %  (" ".join(cll), p.returncode))
@@ -839,8 +841,8 @@
                 "test",
                 "--galaxy_root",
                 self.args.galaxy_root,
-                "--update_test_data",
-                "--docker",
+                "--update_test_data",           
+                "--directory", self.args.tool_dir,
                 xreal,
             ]
             p = subprocess.run(
@@ -848,7 +850,8 @@
                 )
         else:
             cll = ["planemo", "test", "--galaxy_root",
-                self.args.galaxy_root, "--docker",
+                self.args.galaxy_root, 
+            "--directory", self.args.tool_dir,
                 xreal,]
             p = subprocess.run(
                     cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout
@@ -951,6 +954,7 @@
     a("--sysexe", default=None)
     a("--packages", default=None)
     a("--tool_name", default=None)
+    a("--tool_dir", default=None)
     a("--input_files", default=[], action="append")
     a("--output_files", default=[], action="append")
     a("--user_email", default="Unknown")
--- a/toolfactory/rgToolFactory2.xml	Sat Nov 14 06:16:34 2020 +0000
+++ b/toolfactory/rgToolFactory2.xml	Sat Nov 14 08:04:59 2020 +0000
@@ -189,6 +189,7 @@
 --output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL~~~$otab.history_test"
      #end for
 --galaxy_root "$__root_dir__"
+--tool_dir "$__tool_dir__"
  #end if
 ]]></command>
  <configfiles>