From dan@bx.psu.edu Tue Apr 7 10:15:18 2015 From: Daniel Blankenberg To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] a question on data manager and data table Date: Tue, 07 Apr 2015 10:15:18 -0400 Message-ID: In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============0751507383925418015==" --===============0751507383925418015== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hi Rui, The Extract Genomic DNA Tool has not yet been updated to work with tool Data = Tables.=20 Additionally, this tool requires TwoBit formatted files when selecting from b= uilt-in data =E2=80=94 when selecting a FASTA from your history, the fasta fi= le is converted to TwoBit internally in the tool before extracting sequence c= hunks. There is a TwoBit builder Data Manager under development (https://github.com/= galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_bui= lder), that hasn=E2=80=99t made it out to the ToolShed just yet, but it won= =E2=80=99t be helpful until the the Extract Genomic DNA Tool is updated: htt= ps://trello.com/c/8unnSp7H Thanks for using Galaxy, Dan On Apr 7, 2015, at 12:16 AM, Beginner TI wrote: > Hi All, >=20 > I just made a new local instance, installed the fetch_all_fasta data manage= r, downloaded mm9 fasta. Then I noticed the following: >=20 > in tool_data_table_conf.xml, it has: >=20 > > value, dbkey, name, path > >
>=20 > however in shed_tool_data_table_conf.xml, it has: >=20 > > value, dbkey, name, path > > toolshed.g2.bx.psu.edudata_manager_fetch_genome_all_fastadevteamcca219f2b212
>=20 > in tool-data, all_fasta.loc is empty, but in the all_fasta.loc of the shed_= tool entry, it shows: >=20 > mm9 mm9 Mouse July 2007 (NCBI37/mm9) (mm9) /auto/rcf-proj/yc1/= galaxy-suite/galaxy-dist/tool-data/mm9/seq/mm9.fa >=20 > So if I try "Extract Genomic DNA function", I could see the parameter passe= d to the command line is=20 >=20 > -g "/auto/rcf-proj/yc1/galaxy-suite/galaxy-dist/tool-data"=20 >=20 > which does not host the data. It should be at least >=20 > -g "/auto/rcf-proj/yc1/galaxy-suite/galaxy-dist/tool-data/mm9/seq" >=20 > I thought that data manager will automatically populate these loc files? Am= I missing something obvious? I could manually modify tool_data_table_conf.x= ml to let it point to >=20 > /auto/rcf-proj/yc1/galaxy-suite/galaxy-dist/tool-data/toolshed.g2.bx.psu.ed= u/repos/devteam/data_manager_fetch_genome_all_fasta/cca219f2b212/all_fasta.loc >=20 > This would work, but it is ugly. Could someone please give me a hand to fix= this? >=20 > Thanks, > Rui > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ >=20 > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ --===============0751507383925418015== Content-Type: text/html Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="attachment.htm" MIME-Version: 1.0 PGh0bWw+PGhlYWQ+PG1ldGEgaHR0cC1lcXVpdj0iQ29udGVudC1UeXBlIiBjb250ZW50PSJ0ZXh0 L2h0bWwgY2hhcnNldD13aW5kb3dzLTEyNTIiPjwvaGVhZD48Ym9keSBzdHlsZT0id29yZC13cmFw OiBicmVhay13b3JkOyAtd2Via2l0LW5ic3AtbW9kZTogc3BhY2U7IC13ZWJraXQtbGluZS1icmVh azogYWZ0ZXItd2hpdGUtc3BhY2U7Ij5IaSBSdWksPGRpdj48YnI+PC9kaXY+PGRpdj5UaGUgRXh0 cmFjdCBHZW5vbWljIEROQSBUb29sIGhhcyBub3QgeWV0IGJlZW4gdXBkYXRlZCB0byB3b3JrIHdp dGggdG9vbCBEYXRhIFRhYmxlcy4mbmJzcDs8L2Rpdj48ZGl2Pjxicj48L2Rpdj48ZGl2PkFkZGl0 aW9uYWxseSwgdGhpcyB0b29sIHJlcXVpcmVzIFR3b0JpdCBmb3JtYXR0ZWQgZmlsZXMgd2hlbiBz 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