Hi all - It looks like bowtie's wrapper is working incorrectly for a list of dataset pairs. Its expecting all the forward reads in one dataset list and the reverse reads in a separate dataset list.
Instead, I have a list of dataset pairs (for paired-end data). This cannot be provided to bowtie as input. If I correct this, should I create a pull request for it? Alternatively, does someone already have a corrected version of this?
Hi Ryan,
latest wrappers are here: https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 And a PR would be great!
But as far as I can see this is already implemented and you can choose as option `Paired-end Dataset Collection`, isn't it?
Ciao, Bjoern
On 24.06.2015 20:02, Ryan G wrote:
Hi all - It looks like bowtie's wrapper is working incorrectly for a list of dataset pairs. Its expecting all the forward reads in one dataset list and the reverse reads in a separate dataset list.
Instead, I have a list of dataset pairs (for paired-end data). This cannot be provided to bowtie as input. If I correct this, should I create a pull request for it? Alternatively, does someone already have a corrected version of this?
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What Bjoern said - unless you meant the older bowtie1 wrappers. Those have not been updated - I think we decision was made at Penn State to focus on bowtie2 - but if people are still interested in enhancing the bowtie1 wrappers I think a PR would be welcome. There have been some other relatively recent bowtie1 PRs (e.g. from Nicola https://github.com/galaxyproject/tools-devteam/pull/49).
-John
On Thu, Jun 25, 2015 at 3:46 AM, Bjoern Gruening bjoern.gruening@gmail.com wrote:
Hi Ryan,
latest wrappers are here: https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 And a PR would be great!
But as far as I can see this is already implemented and you can choose as option `Paired-end Dataset Collection`, isn't it?
Ciao, Bjoern
On 24.06.2015 20:02, Ryan G wrote:
Hi all - It looks like bowtie's wrapper is working incorrectly for a list of dataset pairs. Its expecting all the forward reads in one dataset list and the reverse reads in a separate dataset list.
Instead, I have a list of dataset pairs (for paired-end data). This cannot be provided to bowtie as input. If I correct this, should I create a pull request for it? Alternatively, does someone already have a corrected version of this?
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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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: https://lists.galaxyproject.org/
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galaxy-dev@lists.galaxyproject.org
-
Bjoern Gruening -
John Chilton -
Ryan G