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 copied to: - tool-data/ (with AND without .sample extension) - tool-data/toolshed.g2.bx.psu.edu/repos/OWNER/REPO/REVISION/ (without .sample extension) 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."