Re: [galaxy-dev] samtools mpileup update
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: http://lists.bx.psu.edu/ -- 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] samtools mpileup update
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: http://lists.bx.psu.edu/ -- 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: http://lists.bx.psu.edu/ -- 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: http://lists.bx.psu.edu/
[galaxy-dev] samtools mpileup update
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: http://lists.bx.psu.edu/
