I've had a bit of a time trying to get Bismark working on our Galaxy instance. The install doesn't work because of the dependency on samtools 0.1.18 but in fact it requires samtools 0.1.19. I have a build of that installed as standard on our system so putting a symlink to that in the place of the samtools built for the bismark wrapper makes it work - I was seeing issues where the BAM file wasn't created and noticed in Bjoern's readme.rst that said it required samtools 0.1.19 or later.
Shane
-- For urgent cases, contact support@biomatters.com
Dr Shane Sturrock shane.sturrock@biomatters.com Senior Scientist Tel: +64 (0) 9 379 5064 76 Anzac Ave Auckland New Zealand
Hi Shane,
that is sadly true. Totally forget to migrate the samtools package to the main toolshed. Will do that week.
Sorry for the inconvenience and thanks for pointing that out! Bjoern
I've had a bit of a time trying to get Bismark working on our Galaxy instance. The install doesn't work because of the dependency on samtools 0.1.18 but in fact it requires samtools 0.1.19. I have a build of that installed as standard on our system so putting a symlink to that in the place of the samtools built for the bismark wrapper makes it work - I was seeing issues where the BAM file wasn't created and noticed in Bjoern's readme.rst that said it required samtools 0.1.19 or later.
Shane
-- For urgent cases, contact support@biomatters.com
Dr Shane Sturrock shane.sturrock@biomatters.com Senior Scientist Tel: +64 (0) 9 379 5064 76 Anzac Ave Auckland New Zealand
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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Shane,
please find a new bismark version with an updated dependency on samtools 0.1.19 here:
http://toolshed.g2.bx.psu.edu/view/bgruening/bismark
Thanks for reporting that issue, Bjoern
I've had a bit of a time trying to get Bismark working on our Galaxy instance. The install doesn't work because of the dependency on samtools 0.1.18 but in fact it requires samtools 0.1.19. I have a build of that installed as standard on our system so putting a symlink to that in the place of the samtools built for the bismark wrapper makes it work - I was seeing issues where the BAM file wasn't created and noticed in Bjoern's readme.rst that said it required samtools 0.1.19 or later.
Shane
-- For urgent cases, contact support@biomatters.com
Dr Shane Sturrock shane.sturrock@biomatters.com Senior Scientist Tel: +64 (0) 9 379 5064 76 Anzac Ave Auckland New Zealand
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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Bjoern,
I've upgraded our machine and confirmed it now works fine. Thanks for that!
Shane
On 22/08/2013, at 5:17 AM, Bjoern Gruening bjoern.gruening@gmail.com wrote:
Hi Shane,
please find a new bismark version with an updated dependency on samtools 0.1.19 here:
http://toolshed.g2.bx.psu.edu/view/bgruening/bismark
Thanks for reporting that issue, Bjoern
I've had a bit of a time trying to get Bismark working on our Galaxy instance. The install doesn't work because of the dependency on samtools 0.1.18 but in fact it requires samtools 0.1.19. I have a build of that installed as standard on our system so putting a symlink to that in the place of the samtools built for the bismark wrapper makes it work - I was seeing issues where the BAM file wasn't created and noticed in Bjoern's readme.rst that said it required samtools 0.1.19 or later.
Shane
-- For urgent cases, contact support@biomatters.com
Dr Shane Sturrock shane.sturrock@biomatters.com Senior Scientist Tel: +64 (0) 9 379 5064 76 Anzac Ave Auckland New Zealand
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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- For urgent cases, contact support@biomatters.com
Dr Shane Sturrock shane.sturrock@biomatters.com Senior Scientist Tel: +64 (0) 9 379 5064 76 Anzac Ave Auckland New Zealand
galaxy-dev@lists.galaxyproject.org
-
Bjoern Gruening -
Björn Grüning -
Shane Sturrock