Share some code (xml) to wrap IGV itself as a Galaxy visualizer
Hi Guys, I am glad to hear form Jim Robinson that exists some code could wrap IGV as a Galaxy visualizer. Recently, i implemented local Galaxy instant and wanted to integrate IGV as a visualizer. I'm looking forward your reply. Regards, Ming
Hi Ming, From Galaxy, you can currently view BAM and VCF (VCF is available in -central, but will be in the next -dist release) files within IGV. To do this on a local set up, you will need to have your Galaxy instance behind a proxy (e.g. nginx or apache); this enables byte-range requests. In the datatypes_conf.xml file, make sure that '<display file="igv/bam.xml" />' and '<display file="igv/vcf.xml" />' are not commented out. Within Galaxy, your BAM or VCF file should have the dbkey set to a build that is configured to be viewable at IGV (see tool-data/shared/igv/igv_build_sites.txt). Please let us know if we can provide additional assistance. Thanks for using Galaxy, Dan On Jan 14, 2012, at 10:09 PM, bt.microzhang@gmail.com wrote:
Hi Guys, I am glad to hear form Jim Robinson that exists some code could wrap IGV as a Galaxy visualizer. Recently, i implemented local Galaxy instant and wanted to integrate IGV as a visualizer. I'm looking forward your reply.
Regards,
Ming ___________________________________________________________ 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:
Dan, any idea when the next dist release is scheduled? We need to upgrade our wur instance seriously and from then keep up the pace, but it would be a pity if we upgrade and extensively test it now, while the new release is out a few days later. The latest is from November 18th right?! Thanks Alex ________________________________ Van: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] namens Daniel Blankenberg [dan@bx.psu.edu] Verzonden: dinsdag 17 januari 2012 15:09 Aan: igv-help@googlegroups.com CC: galaxy-dev@lists.bx.psu.edu; jrobinso@broadinstitute.org Onderwerp: Re: [galaxy-dev] Share some code (xml) to wrap IGV itself as a Galaxy visualizer Hi Ming,
From Galaxy, you can currently view BAM and VCF (VCF is available in -central, but will be in the next -dist release) files within IGV. To do this on a local set up, you will need to have your Galaxy instance behind a proxy (e.g. nginx or apache); this enables byte-range requests. In the datatypes_conf.xml file, make sure that '<display file="igv/bam.xml" />' and '<display file="igv/vcf.xml" />' are not commented out. Within Galaxy, your BAM or VCF file should have the dbkey set to a build that is configured to be viewable at IGV (see tool-data/shared/igv/igv_build_sites.txt).
Please let us know if we can provide additional assistance. Thanks for using Galaxy, Dan On Jan 14, 2012, at 10:09 PM, bt.microzhang@gmail.com<mailto:bt.microzhang@gmail.com> wrote: Hi Guys, I am glad to hear form Jim Robinson that exists some code could wrap IGV as a Galaxy visualizer. Recently, i implemented local Galaxy instant and wanted to integrate IGV as a visualizer. I'm looking forward your reply. Regards, Ming ___________________________________________________________ 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/
Hi Alex, Yes, thats the current -dist. I hope I don't regret saying this, but we are pushing for a new release coming real soon, so you may want to hold off on the update if it will require extensive testing on your end. Thanks for using Galaxy, Dan On Jan 17, 2012, at 9:13 AM, Bossers, Alex wrote:
Dan, any idea when the next dist release is scheduled? We need to upgrade our wur instance seriously and from then keep up the pace, but it would be a pity if we upgrade and extensively test it now, while the new release is out a few days later. The latest is from November 18th right?! Thanks Alex
________________________________ Van: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] namens Daniel Blankenberg [dan@bx.psu.edu] Verzonden: dinsdag 17 januari 2012 15:09 Aan: igv-help@googlegroups.com CC: galaxy-dev@lists.bx.psu.edu; jrobinso@broadinstitute.org Onderwerp: Re: [galaxy-dev] Share some code (xml) to wrap IGV itself as a Galaxy visualizer
Hi Ming,
From Galaxy, you can currently view BAM and VCF (VCF is available in -central, but will be in the next -dist release) files within IGV. To do this on a local set up, you will need to have your Galaxy instance behind a proxy (e.g. nginx or apache); this enables byte-range requests. In the datatypes_conf.xml file, make sure that '<display file="igv/bam.xml" />' and '<display file="igv/vcf.xml" />' are not commented out. Within Galaxy, your BAM or VCF file should have the dbkey set to a build that is configured to be viewable at IGV (see tool-data/shared/igv/igv_build_sites.txt).
Please let us know if we can provide additional assistance.
Thanks for using Galaxy,
Dan
On Jan 14, 2012, at 10:09 PM, bt.microzhang@gmail.com<mailto:bt.microzhang@gmail.com> wrote:
Hi Guys, I am glad to hear form Jim Robinson that exists some code could wrap IGV as a Galaxy visualizer. Recently, i implemented local Galaxy instant and wanted to integrate IGV as a visualizer. I'm looking forward your reply.
Regards,
Ming ___________________________________________________________ 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:
Hi Dan, thanks for the response. Does Galaxy index VCF files, for example with tabix of the "tribble" library? IGV currently requires indexes for VCF files, mainly because the ones we generate here are huge. This could be relaxed for smaller VCF files, and I have that on my list. best, Jim
Hi Ming,
From Galaxy, you can currently view BAM and VCF (VCF is available in -central, but will be in the next -dist release) files within IGV. To do this on a local set up, you will need to have your Galaxy instance behind a proxy (e.g. nginx or apache); this enables byte-range requests. In the datatypes_conf.xml file, make sure that '<display file="igv/bam.xml" />' and '<display file="igv/vcf.xml" />' are not commented out. Within Galaxy, your BAM or VCF file should have the dbkey set to a build that is configured to be viewable at IGV (see tool-data/shared/igv/igv_build_sites.txt).
Please let us know if we can provide additional assistance.
Thanks for using Galaxy,
Dan
On Jan 14, 2012, at 10:09 PM, bt.microzhang@gmail.com <mailto:bt.microzhang@gmail.com> wrote:
Hi Guys, I am glad to hear form Jim Robinson that exists some code could wrap IGV as a Galaxy visualizer. Recently, i implemented local Galaxy instant and wanted to integrate IGV as a visualizer. I'm looking forward your reply.
Regards,
Ming ___________________________________________________________ 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:
Hi Jim, Yes, Galaxy ships the vcf files bgzip compressed (filename.vcf.gz) and makes a tabix index available along side (filename.vcf.gz.tbi). In the case of Galaxy, the pysam package is used to create the tabix index. Thanks, Dan On Jan 17, 2012, at 9:44 AM, Jim Robinson wrote:
Hi Dan, thanks for the response. Does Galaxy index VCF files, for example with tabix of the "tribble" library? IGV currently requires indexes for VCF files, mainly because the ones we generate here are huge. This could be relaxed for smaller VCF files, and I have that on my list.
best,
Jim
Hi Ming,
From Galaxy, you can currently view BAM and VCF (VCF is available in -central, but will be in the next -dist release) files within IGV. To do this on a local set up, you will need to have your Galaxy instance behind a proxy (e.g. nginx or apache); this enables byte-range requests. In the datatypes_conf.xml file, make sure that '<display file="igv/bam.xml" />' and '<display file="igv/vcf.xml" />' are not commented out. Within Galaxy, your BAM or VCF file should have the dbkey set to a build that is configured to be viewable at IGV (see tool-data/shared/igv/igv_build_sites.txt).
Please let us know if we can provide additional assistance.
Thanks for using Galaxy,
Dan
On Jan 14, 2012, at 10:09 PM, bt.microzhang@gmail.com wrote:
Hi Guys, I am glad to hear form Jim Robinson that exists some code could wrap IGV as a Galaxy visualizer. Recently, i implemented local Galaxy instant and wanted to integrate IGV as a visualizer. I'm looking forward your reply.
Regards,
Ming ___________________________________________________________ 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:
participants (4)
-
Bossers, Alex -
bt.microzhang＠gmail.com -
Daniel Blankenberg -
Jim Robinson