2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/be37937a0b5b/ changeset: be37937a0b5b user: jgoecks date: 2012-12-07 16:15:48 summary: Add needed import. affected #: 1 file diff -r ad6d34f4decb896e65d988cdd71a09f3fad62722 -r be37937a0b5b05c6047720758bf330087c099e6c lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -3,6 +3,7 @@ """ import logging, os, string, shutil, urllib, re, socket from galaxy import util, datatypes, jobs, web, util +from galaxy.visualization.data_providers.genome import FeatureLocationIndexDataProvider from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin, get_highest_priority_msg, messages from galaxy.web.framework.helpers import is_true https://bitbucket.org/galaxy/galaxy-central/changeset/8305907fa231/ changeset: 8305907fa231 user: jgoecks date: 2012-12-07 16:18:50 summary: Fixes for bam_to_summary_tree converter: (a) remove deprecated page tags and (b) use bai from metadata rather than from dependency injection. affected #: 1 file diff -r be37937a0b5b05c6047720758bf330087c099e6c -r 8305907fa2312da14cf4d500fba1675a169b5517 lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.xml --- a/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.xml +++ b/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.xml @@ -1,11 +1,10 @@ <tool id="CONVERTER_bam_to_summary_tree_0" name="Convert BAM to Summary Tree" version="1.0.0" hidden="true"> -<!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> --> - <command interpreter="python">sam_or_bam_to_summary_tree_converter.py --bam $input1 $bai $output1</command> + <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> --> + <command interpreter="python"> + sam_or_bam_to_summary_tree_converter.py --bam $input1 $input1.metadata.bam_index $output1 + </command><inputs> - <page> - <param format="bam" name="input1" type="data" label="Choose BAM file"/> - <param format="bai" name="bai" type="data" label="BAI index file"/> - </page> + <param format="bam" name="input1" type="data" label="Choose BAM file"/></inputs><outputs><data format="summary_tree" name="output1"/> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.