Re: [galaxy-dev] which .loc file for "SAM to BAM"?
Sorry for my unclear sentence, I meant the page you pointed me too. regards, Andreas On 01.11.2012 14:50, Carlos Borroto wrote: Well is not my page, I'm not directly related to Galaxy. Still, I think Galaxy Project would be happy to receive updates to the wiki, maybe a complete table can be added to the page you are mentioning. On Thu, Nov 1, 2012 at 4:27 AM, Andreas Kuntzagk wrote: Hi, thank you for the pointer. I was only looking at this wiki page: http://wiki.g2.bx.psu.edu/Admin/Data%20Integration Maybe this should point to your page? regards, Andreas On 31.10.2012 17:50, Carlos Borroto wrote: On Wed, Oct 31, 2012 at 11:30 AM, Andreas Kuntzagk wrote: Hi, I'm still setting up a local galaxy. Currently I'm testing the setup of NGS tools. If I try "SAM to BAM" for a BAM file that has "hg18" set as build I get a message that "Sequences are not currently available for the specified build." I guess that I have either to manipulate one of the .loc files (but which?) or have to download additional data from rsync server. (I already have the tool-data/shared/hg18 completely) The .loc file you want to modify is 'tool-data/sam_fa_indices.loc'. You can find information about this subject in the wiki[1]. Although the table there is not complete, so you could always find the right xml under 'tools' and poke inside to find a line like this one: [1]http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup And I agree, dealing with .loc files is quite cumbersome. Hope it helps, Carlos -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich ___ 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/
Re: [galaxy-dev] which .loc file for "SAM to BAM"?
Well is not my page, I'm not directly related to Galaxy. Still, I think Galaxy Project would be happy to receive updates to the wiki, maybe a complete table can be added to the page you are mentioning. On Thu, Nov 1, 2012 at 4:27 AM, Andreas Kuntzagk wrote: > Hi, > > thank you for the pointer. > I was only looking at this wiki page: > http://wiki.g2.bx.psu.edu/Admin/Data%20Integration > > Maybe this should point to your page? > > regards, Andreas > > > On 31.10.2012 17:50, Carlos Borroto wrote: >> >> On Wed, Oct 31, 2012 at 11:30 AM, Andreas Kuntzagk >> wrote: >>> >>> Hi, >>> >>> I'm still setting up a local galaxy. Currently I'm testing the setup of >>> NGS >>> tools. If I try "SAM to BAM" for a BAM file that has "hg18" set as build >>> I >>> get a message that >>> "Sequences are not currently available for the specified build." I guess >>> that I have either to manipulate one of the .loc files (but which?) or >>> have >>> to download additional data from rsync server. >>> (I already have the tool-data/shared/hg18 completely) >>> >> >> The .loc file you want to modify is 'tool-data/sam_fa_indices.loc'. >> You can find information about this subject in the wiki[1]. Although >> the table there is not complete, so you could always find the right >> xml under 'tools' and poke inside to find a line like this one: >> > filename="sam_fa_indices.loc" metadata_name="dbkey" >> metadata_column="1" message="Sequences are not currently available for >> the specified build." line_startswith="index" /> >> >> [1]http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup >> >> And I agree, dealing with .loc files is quite cumbersome. >> >> Hope it helps, >> Carlos >> > > -- > Andreas Kuntzagk > > SystemAdministrator > > Berlin Institute for Medical Systems Biology at the > Max-Delbrueck-Center for Molecular Medicine > Robert-Roessle-Str. 10, 13125 Berlin, Germany > > http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich ___ 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/
Re: [galaxy-dev] which .loc file for "SAM to BAM"?
Hi, thank you for the pointer. I was only looking at this wiki page: http://wiki.g2.bx.psu.edu/Admin/Data%20Integration Maybe this should point to your page? regards, Andreas On 31.10.2012 17:50, Carlos Borroto wrote: On Wed, Oct 31, 2012 at 11:30 AM, Andreas Kuntzagk wrote: Hi, I'm still setting up a local galaxy. Currently I'm testing the setup of NGS tools. If I try "SAM to BAM" for a BAM file that has "hg18" set as build I get a message that "Sequences are not currently available for the specified build." I guess that I have either to manipulate one of the .loc files (but which?) or have to download additional data from rsync server. (I already have the tool-data/shared/hg18 completely) The .loc file you want to modify is 'tool-data/sam_fa_indices.loc'. You can find information about this subject in the wiki[1]. Although the table there is not complete, so you could always find the right xml under 'tools' and poke inside to find a line like this one: [1]http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup And I agree, dealing with .loc files is quite cumbersome. Hope it helps, Carlos -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich ___ 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/
Re: [galaxy-dev] which .loc file for "SAM to BAM"?
On Wed, Oct 31, 2012 at 11:30 AM, Andreas Kuntzagk wrote: > Hi, > > I'm still setting up a local galaxy. Currently I'm testing the setup of NGS > tools. If I try "SAM to BAM" for a BAM file that has "hg18" set as build I > get a message that > "Sequences are not currently available for the specified build." I guess > that I have either to manipulate one of the .loc files (but which?) or have > to download additional data from rsync server. > (I already have the tool-data/shared/hg18 completely) > The .loc file you want to modify is 'tool-data/sam_fa_indices.loc'. You can find information about this subject in the wiki[1]. Although the table there is not complete, so you could always find the right xml under 'tools' and poke inside to find a line like this one: [1]http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup And I agree, dealing with .loc files is quite cumbersome. Hope it helps, Carlos ___ 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/
[galaxy-dev] which .loc file for "SAM to BAM"?
Hi, I'm still setting up a local galaxy. Currently I'm testing the setup of NGS tools. If I try "SAM to BAM" for a BAM file that has "hg18" set as build I get a message that "Sequences are not currently available for the specified build." I guess that I have either to manipulate one of the .loc files (but which?) or have to download additional data from rsync server. (I already have the tool-data/shared/hg18 completely) regards, Andreas Btw. Do you have any plans to ease the pain on adding additional builds? Something simpler than having to add one line for each build*tool combo? These lines seem very redundant to me. -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich ___ 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/
