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." Suggestions? Thanks, Nicola ___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
