Mercurial > repos > gga > apollo_fetch_jbrowse
changeset 5:0c5347327b0c draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 70fbb41d4c6b0a08a7bed4849a5ae7c865e1ab1e
| author | gga |
|---|---|
| date | Mon, 12 Mar 2018 06:27:57 -0400 |
| parents | 2e4927caab01 |
| children | 3877c75bd492 |
| files | README.rst create_account.py create_features_from_gff3.py export.py fetch_organism_jbrowse.xml macros.xml webapollo.py |
| diffstat | 7 files changed, 11 insertions(+), 14 deletions(-) [+] |
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--- a/README.rst Thu Feb 08 11:35:39 2018 -0500 +++ b/README.rst Mon Mar 12 06:27:57 2018 -0400 @@ -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
--- a/create_account.py Thu Feb 08 11:35:39 2018 -0500 +++ b/create_account.py Mon Mar 12 06:27:57 2018 -0400 @@ -4,7 +4,8 @@ import argparse import random import time -from builtins import range, str + +from six.moves.builtins import str from webapollo import WAAuth, WebApolloInstance
--- a/create_features_from_gff3.py Thu Feb 08 11:35:39 2018 -0500 +++ b/create_features_from_gff3.py Mon Mar 12 06:27:57 2018 -0400 @@ -3,10 +3,11 @@ import logging import sys import time -from builtins import str 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) log = logging.getLogger(__name__)
--- a/export.py Thu Feb 08 11:35:39 2018 -0500 +++ b/export.py Mon Mar 12 06:27:57 2018 -0400 @@ -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:
--- a/fetch_organism_jbrowse.xml Thu Feb 08 11:35:39 2018 -0500 +++ b/fetch_organism_jbrowse.xml Mon Mar 12 06:27:57 2018 -0400 @@ -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>
--- a/macros.xml Thu Feb 08 11:35:39 2018 -0500 +++ b/macros.xml Mon Mar 12 06:27:57 2018 -0400 @@ -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>
--- a/webapollo.py Thu Feb 08 11:35:39 2018 -0500 +++ b/webapollo.py Mon Mar 12 06:27:57 2018 -0400 @@ -7,20 +7,18 @@ 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: