1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/f265985eaca2/
changeset: f265985eaca2
user: smcmanus
date: 2012-10-23 00:06:09
summary: Fixed bug in accessing /folders content as non-admin. Added comment.
affected #: 2 files
diff -r 97816731e24bff2d825c7713787df2b0f2fc445f -r f265985eaca2a5fad402810c2cf030ec26f89e97 lib/galaxy/webapps/galaxy/api/folder_contents.py
--- a/lib/galaxy/webapps/galaxy/api/folder_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py
@@ -59,7 +59,7 @@
# TODO: Find the API's path to this folder if necessary.
# This was needed in recursive descent, but it's not needed
# for "ls"-style content checking:
- if not folder or not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder ) ):
+ if not folder or not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ):
trans.response.status = 400
return "Invalid folder id ( %s ) specified." % str( folder_id )
diff -r 97816731e24bff2d825c7713787df2b0f2fc445f -r f265985eaca2a5fad402810c2cf030ec26f89e97 lib/galaxy/webapps/galaxy/api/folders.py
--- a/lib/galaxy/webapps/galaxy/api/folders.py
+++ b/lib/galaxy/webapps/galaxy/api/folders.py
@@ -50,7 +50,6 @@
moved here.
o payload's relevant params:
- - create_type: "file" or "folder" (required)
- folder_id: This is the parent folder's id (required)
"""
log.debug( "FoldersController.create: enter" )
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.
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/60fee5ee38fa/
changeset: 60fee5ee38fa
user: jgoecks
date: 2012-10-22 16:52:48
summary: Enable Tophat, Tophat2, and Cuffdiff to accept gene annotations in GFF3 format. Thanks to Jim Johnson.
affected #: 3 files
diff -r 1dc4dd32eaf8b38da3e66bdc2de287f907b3605e -r 60fee5ee38fada926d010971e49623367b78362e tools/ngs_rna/cuffdiff_wrapper.xml
--- a/tools/ngs_rna/cuffdiff_wrapper.xml
+++ b/tools/ngs_rna/cuffdiff_wrapper.xml
@@ -72,7 +72,7 @@
</command><inputs>
- <param format="gtf" name="gtf_input" type="data" label="Transcripts" help="A transcript GTF file produced by cufflinks, cuffcompare, or other source."/>
+ <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" help="A transcript GTF file produced by cufflinks, cuffcompare, or other source."/><conditional name="group_analysis"><param name="do_groups" type="select" label="Perform replicate analysis" help="Perform cuffdiff with replicates in each group."><option value="No">No</option>
diff -r 1dc4dd32eaf8b38da3e66bdc2de287f907b3605e -r 60fee5ee38fada926d010971e49623367b78362e tools/ngs_rna/tophat2_wrapper.xml
--- a/tools/ngs_rna/tophat2_wrapper.xml
+++ b/tools/ngs_rna/tophat2_wrapper.xml
@@ -210,7 +210,7 @@
</param><when value="No" /><when value="Yes">
- <param format="gtf" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/>
+ <param format="gtf,gff3" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/></when></conditional><conditional name="raw_juncs">
diff -r 1dc4dd32eaf8b38da3e66bdc2de287f907b3605e -r 60fee5ee38fada926d010971e49623367b78362e tools/ngs_rna/tophat_wrapper.xml
--- a/tools/ngs_rna/tophat_wrapper.xml
+++ b/tools/ngs_rna/tophat_wrapper.xml
@@ -224,7 +224,7 @@
</param><when value="No" /><when value="Yes">
- <param format="gtf" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/>
+ <param format="gtf,gff3" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/></when></conditional><conditional name="raw_juncs">
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.