I wrote a script to compare these files mainly to be able to remove tool's sections and add our own, but when used to compare main vs sample I've got 2 sections and 3 tools that are in main but not in sample. Here is the list:
WARNING: --- cshl_library_information: Section from tool_conf.xml.main is not in tool_conf.xml.sample. It will be ignored. WARNING: --- ngs_mapping: Section from tool_conf.xml.main is not in tool_conf.xml.sample. It will be ignored. WARNING: --- filters/condense_characters.xml: Tool from section textutil is not in tool_conf.xml.sample. It will be ignored. WARNING: --- stats/dna_filtering.xml: Tool from section filter is not in tool_conf.xml.sample. It will be ignored. WARNING: --- data_source/hapmapmart.xml: Tool from section rgdat is not in tool_conf.xml.sample. It will be ignored.
A list of tools and sections that are in sample file but not in main:
WARNING: +++ data_source/ucsc_tablebrowser_test.xml: New Tool in section getext. It will be added. WARNING: +++ data_source/microbial_import.xml: New Tool in section getext. It will be added. WARNING: +++ data_source/biomart_test.xml: New Tool in section getext. It will be added. WARNING: +++ data_source/cbi_rice_mart.xml: New Tool in section getext. It will be added. WARNING: +++ data_source/flymine_test.xml: New Tool in section getext. It will be added. WARNING: +++ data_source/metabolicmine.xml: New Tool in section getext. It will be added. WARNING: +++ data_source/wormbase_test.xml: New Tool in section getext. It will be added. WARNING: +++ data_source/epigraph_import_test.xml: New Tool in section getext. It will be added. WARNING: +++ data_source/hbvar.xml: New Tool in section getext. It will be added. WARNING: +++ data_source/genomespace_file_browser_prod.xml: New Tool in section getext. It will be added. WARNING: +++ validation/fix_errors.xml: New Tool in section getext. It will be added. WARNING: +++ data_destination/epigraph_test.xml: New Tool in section send. It will be added. WARNING: +++ stats/dna_filtering.xml: New Tool in section textutil. It will be added. WARNING: +++ new_operations/tables_arithmetic_operations.xml: New Tool in section textutil. It will be added. WARNING: +++ filters/axt_to_concat_fasta.xml: New Tool in section convert. It will be added. WARNING: +++ filters/axt_to_fasta.xml: New Tool in section convert. It will be added. WARNING: +++ filters/axt_to_lav.xml: New Tool in section convert. It will be added. WARNING: +++ filters/lav_to_bed.xml: New Tool in section convert. It will be added. WARNING: +++ filters/wiggle_to_simple.xml: New Tool in section convert. It will be added. WARNING: +++ filters/gtf2bedgraph.xml: New Tool in section convert. It will be added. WARNING: +++ maf/maf_split_by_species.xml: New Tool in section fetchAlign. It will be added. WARNING: +++ regVariation/t_test_two_samples.xml: New Tool in section stats. It will be added. WARNING: +++ regVariation/compute_q_values.xml: New Tool in section stats. It will be added. WARNING: +++ stats/MINE.xml: New Tool in section stats. It will be added. WARNING: +++ stats/count_gff_features.xml: New Tool in section stats. It will be added. WARNING: +++ dwt: New Section. Please update list of unwanted sections, otherwise it will be added. WARNING: +++ plotting/bar_chart.xml: New Tool in section plots. It will be added. WARNING: +++ visualization/LAJ.xml: New Tool in section plots. It will be added. WARNING: +++ regVariation/delete_overlapping_indels.xml: New Tool in section regVar. It will be added. WARNING: +++ regVariation/compute_motifs_frequency.xml: New Tool in section regVar. It will be added. WARNING: +++ regVariation/compute_motif_frequencies_for_all_motifs.xml: New Tool in section regVar. It will be added. WARNING: +++ regVariation/categorize_elements_satisfying_criteria.xml: New Tool in section regVar. It will be added. WARNING: +++ regVariation/draw_stacked_barplots.xml: New Tool in section regVar. It will be added. WARNING: +++ hyphy/hyphy_dnds_wrapper.xml: New Tool in section hyphy. It will be added. WARNING: +++ evolution/codingSnps.xml: New Tool in section hyphy. It will be added. WARNING: +++ evolution/add_scores.xml: New Tool in section hyphy. It will be added. WARNING: +++ meme/meme.xml: New Tool in section motifs. It will be added. WARNING: +++ meme/fimo.xml: New Tool in section motifs. It will be added.
WARNING: +++ ncbi_blast_plus_tools: New Section. Please update list of unwanted sections, otherwise it will be added. WARNING: +++ NGS_QC: New Section. Please update list of unwanted sections, otherwise it will be added. WARNING: +++ solexa_tools: New Section. Please update list of unwanted sections, otherwise it will be added. WARNING: +++ indels/indel_table.xml: New Tool in section indel_analysis. It will be added. WARNING: +++ ngs_rna/tophat_color_wrapper.xml: New Tool in section ngs-rna-tools. It will be added. WARNING: +++ variant_detection: New Section. Please update list of unwanted sections, otherwise it will be added. WARNING: +++ peak_calling/ccat_wrapper.xml: New Tool in section peak_calling. It will be added. WARNING: +++ ngs-simulation: New Section. Please update list of unwanted sections, otherwise it will be added. WARNING: +++ vcf_tools: New Section. Please update list of unwanted sections, otherwise it will be added.
Is this correct? Thanks to let me know. Cheers, Anne.
On 27 Mar 2012, at 16:57, Anne Pajon wrote:
Got it. Thanks!
On 27 Mar 2012, at 16:53, Greg Von Kuster wrote:
We have a buildbot set up that runs our functional tests against various platforms / environments. The .sample file used by the buildbot tests everything. The tool_conf.xml.main contains a subset of everything that is tested.
On Mar 27, 2012, at 11:48 AM, Anne Pajon wrote:
Hi Nate,
Thanks but I am still confused... sorry. Why these two files are different then? Are you not running the functional tests on all the tools available at the public server?
Anne.
On 27 Mar 2012, at 16:33, Nate Coraor wrote:
On Mar 27, 2012, at 11:17 AM, Anne Pajon wrote:
Hi,
I would like to know which tool_conf.xml to use, and would like to know the difference between the main and the sample one. I know that the functional tests are running against the tool_conf.xml.sample but what tool_conf.xml.main is used for?
Hi Anne,
tool_conf.xml.main is used by the public server (Galaxy Main) at usegalaxy.org.
--nate
Thanks. Anne. -- Anne Pajon, Ph.D. Cancer Research UK - Cambridge Research Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon@cancer.org.uk | +44 (0)1223 404 334
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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:
-- Anne Pajon, Ph.D. Cancer Research UK - Cambridge Research Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon@cancer.org.uk | +44 (0)1223 404 334
NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose.
We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered in England and Wales Company Registered Number: 4325234. Registered Charity Number: 1089464 and Scotland SC041666 Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD.
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:
-- Anne Pajon, Ph.D. Cancer Research UK - Cambridge Research Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon@cancer.org.uk | +44 (0)1223 404 334
NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose.
We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered in England and Wales Company Registered Number: 4325234. Registered Charity Number: 1089464 and Scotland SC041666 Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD.