Repository 'apollo_fetch_jbrowse'
hg clone https://toolshed.g2.bx.psu.edu/repos/gga/apollo_fetch_jbrowse

Changeset 4:9968eec7430e (2018-03-12)
Previous changeset 3:20c6db7856c6 (2017-09-20) Next changeset 5:1a2976c6b161 (2018-08-31)
Commit message:
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 70fbb41d4c6b0a08a7bed4849a5ae7c865e1ab1e
modified:
README.rst
create_account.py
create_features_from_gff3.py
export.py
fetch_organism_jbrowse.xml
macros.xml
webapollo.py
b
diff -r 20c6db7856c6 -r 9968eec7430e README.rst
--- a/README.rst Wed Sep 20 09:44:15 2017 -0400
+++ b/README.rst Mon Mar 12 06:30:56 2018 -0400
b
@@ -15,7 +15,7 @@
 .. code:: bash
 
     . /path/to/galaxy/.venv/bin/activate
-    pip install future biopython bcbio-gff
+    pip install six biopython bcbio-gff
     deactivate
 
 Environment
b
diff -r 20c6db7856c6 -r 9968eec7430e create_account.py
--- a/create_account.py Wed Sep 20 09:44:15 2017 -0400
+++ b/create_account.py Mon Mar 12 06:30:56 2018 -0400
b
@@ -5,7 +5,7 @@
 import random
 import time
 
-from builtins import range, str
+from six.moves.builtins import str
 
 from webapollo import WAAuth, WebApolloInstance
 
b
diff -r 20c6db7856c6 -r 9968eec7430e create_features_from_gff3.py
--- a/create_features_from_gff3.py Wed Sep 20 09:44:15 2017 -0400
+++ b/create_features_from_gff3.py Mon Mar 12 06:30:56 2018 -0400
b
@@ -4,9 +4,9 @@
 import sys
 import time
 
-from builtins import str
+from BCBio import GFF
 
-from BCBio import GFF
+from six.moves.builtins import str
 
 from webapollo import AssertUser, GuessOrg, OrgOrGuess, WAAuth, WebApolloInstance, featuresToFeatureSchema, retry
 logging.basicConfig(level=logging.INFO)
b
diff -r 20c6db7856c6 -r 9968eec7430e export.py
--- a/export.py Wed Sep 20 09:44:15 2017 -0400
+++ b/export.py Mon Mar 12 06:30:56 2018 -0400
b
@@ -9,11 +9,8 @@
 
 from Bio import SeqIO
 
-from future import standard_library
-
 from webapollo import CnOrGuess, GuessCn, WAAuth, WebApolloInstance
 
-standard_library.install_aliases()
 try:
     import StringIO as io
 except ImportError:
b
diff -r 20c6db7856c6 -r 9968eec7430e fetch_organism_jbrowse.xml
--- a/fetch_organism_jbrowse.xml Wed Sep 20 09:44:15 2017 -0400
+++ b/fetch_organism_jbrowse.xml Mon Mar 12 06:30:56 2018 -0400
b
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="fetch_jbrowse" name="Retrieve JBrowse" version="3.2" profile="16.04">
+<tool id="fetch_jbrowse" name="Retrieve JBrowse" version="3.3" profile="16.04">
   <description>for an organism, from Apollo</description>
   <macros>
     <import>macros.xml</import>
b
diff -r 20c6db7856c6 -r 9968eec7430e macros.xml
--- a/macros.xml Wed Sep 20 09:44:15 2017 -0400
+++ b/macros.xml Mon Mar 12 06:30:56 2018 -0400
b
@@ -6,7 +6,7 @@
       <requirement type="package" version="1.65">biopython</requirement>
       <requirement type="package" version="0.6.2">bcbiogff</requirement>
       <requirement type="package" version="2.12.4">requests</requirement>
-      <requirement type="package" version="0.16.0">future</requirement>
+      <requirement type="package" version="1.11.0">six</requirement>
       <yield/>
     </requirements>
   </xml>
b
diff -r 20c6db7856c6 -r 9968eec7430e webapollo.py
--- a/webapollo.py Wed Sep 20 09:44:15 2017 -0400
+++ b/webapollo.py Mon Mar 12 06:30:56 2018 -0400
b
@@ -6,22 +6,19 @@
 import logging
 import os
 import time
-
 from abc import abstractmethod
-from builtins import next
-from builtins import object
-from builtins import str
 
 from BCBio import GFF
 
 from Bio import SeqIO
 
-from future import standard_library
-
 import requests
 
+from six.moves.builtins import next
+from six.moves.builtins import object
+from six.moves.builtins import str
 
-standard_library.install_aliases()
+
 try:
     import StringIO as io
 except BaseException: