Greg Von Kuster <greg@...> writes:
> On Nov 9, 2012, at 12:56 AM, Derrick Lin wrote:
> > Also how does this change affect the existing shed tools like BWA that
is using tool_data_table_conf.xml?
> The existing shed tools will contiue to function as usual, but entries for
them will be in the tool_data_table_conf.xml file. ANy new tools installed
from the tool shed that use entries like this will be added to the new
shed_tool_data_table_conf.xml file. Entries from both of these files are
loaded into the ToolDataTableManager. The intent is for the Galaxy admin to
be able to manuall make changes to the tool_data_table_conf.xml file and not
have them munged by the tool shed's installation process. This is the same
approach used for the tool_conf.xml file, where the Galaxy tool shed
repository installation process uses the shed_tool_conf.xml file.
Reviving an old thread...
I noticed that when I install a repository from the Tool Shed which contains
a tool_data_table_conf.xml.sample , the sample files mentioned therein are
- tool-data/ (with AND without .sample extension)
- tool-data/toolshed.g2.bx.psu.edu/repos/OWNER/REPO/REVISION/ (without
The tool_data_table_conf.xml file in
tool-data/toolshed.g2.bx.psu.edu/repos/OWNER/REPO/REVISION/ references the
files in the same directory, so I find the duplication confusing.
Moreover, there is an increasing number of repositories which install the
same .loc files, e.g.:
- the 4 cufflinks tools plus sam_pileup, sam_to_bam and samtools_mpileup
install fasta_indexes.loc ;
- blat, lastz and lastz_paired_reads install lastz_seqs.loc .
I suppose it was made to prevent repositories from getting in each other's
way, but I see 2 problems:
- system administrators have to manually hard-link these files;
- duplications in shed_tool_data_table_conf.xml generate errors like:
"galaxy.tools.data ERROR 2014-01-17 15:29:41,409 Attempted to add fields
(['hg19full', 'hg19', 'Human Feb. 2009 (GRCh37/hg19) (hg19) Full',
'/mnt/genome/hg19/sam_index/hg19full/hg19full.fa']) to data table
'fasta_indexes', but this entry already exists and allow_duplicates is False."
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at: