Is there any good reason why Galaxy can't use a more recent version of samtools? The only difference I can see is the mpileup command. The algorithm by which mpileup finds SNPs is a little different. Does anyone know if the file format has changed? The only files that need to change are sam_pileup.py and sam_pileup.xml.
David Hoover Helix Systems Staff http://helix.nih.gov
Hello David,
An update is planned, but we can't provide an exact time-line yet. To track the issue, this bitbucket ticket can be followed: https://bitbucket.org/galaxy/galaxy-central/issue/524/
Apologies for the delay in reply,
Best,
Jen Galaxy team
On 8/23/11 9:10 AM, David Hoover wrote:
Is there any good reason why Galaxy can't use a more recent version of samtools? The only difference I can see is the mpileup command. The algorithm by which mpileup finds SNPs is a little different. Does anyone know if the file format has changed? The only files that need to change are sam_pileup.py and sam_pileup.xml.
David Hoover Helix Systems Staff http://helix.nih.gov ___________________________________________________________ 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:
I have an mpileup tool for Galaxy I've developed. After a little more testing I may be able to share it.
the tool also converts the bcl output of mpileup to vcf
On Oct 12, 2011, at 2:41 PM, Jennifer Jackson wrote:
Hello David,
An update is planned, but we can't provide an exact time-line yet. To track the issue, this bitbucket ticket can be followed: https://bitbucket.org/galaxy/galaxy-central/issue/524/
Apologies for the delay in reply,
Best,
Jen Galaxy team
On 8/23/11 9:10 AM, David Hoover wrote:
Is there any good reason why Galaxy can't use a more recent version of samtools? The only difference I can see is the mpileup command. The algorithm by which mpileup finds SNPs is a little different. Does anyone know if the file format has changed? The only files that need to change are sam_pileup.py and sam_pileup.xml.
David Hoover Helix Systems Staff http://helix.nih.gov ___________________________________________________________ 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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support ___________________________________________________________ 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:
-- Glen L. Beane Senior Software Engineer The Jackson Laboratory (207) 288-6153
Glen:
Please, contribute it to Tool Shed once you are done with testing. This will be much appreciated.
Thanks!
anton
Anton Nekrutenko http://galaxyproject.org
On Oct 12, 2011, at 4:00 PM, Glen Beane wrote:
I have an mpileup tool for Galaxy I've developed. After a little more testing I may be able to share it.
the tool also converts the bcl output of mpileup to vcf
On Oct 12, 2011, at 2:41 PM, Jennifer Jackson wrote:
Hello David,
An update is planned, but we can't provide an exact time-line yet. To track the issue, this bitbucket ticket can be followed: https://bitbucket.org/galaxy/galaxy-central/issue/524/
Apologies for the delay in reply,
Best,
Jen Galaxy team
On 8/23/11 9:10 AM, David Hoover wrote:
Is there any good reason why Galaxy can't use a more recent version of samtools? The only difference I can see is the mpileup command. The algorithm by which mpileup finds SNPs is a little different. Does anyone know if the file format has changed? The only files that need to change are sam_pileup.py and sam_pileup.xml.
David Hoover Helix Systems Staff http://helix.nih.gov ___________________________________________________________ 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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support ___________________________________________________________ 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:
-- Glen L. Beane Senior Software Engineer The Jackson Laboratory (207) 288-6153
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:
galaxy-dev@lists.galaxyproject.org
-
Anton Nekrutenko -
David Hoover -
Glen Beane -
Jennifer Jackson