More bug fixes, and a paired-end TopHat tool.
Available here:
http://cancan.cshl.edu/labmembers/gordon/files/cshl_rnaseq_2011_04_04.tar.bz2
See the interface here:
http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_tophat_pe1
Comments are very welcomed,
Cufflinks is next,
-gordon
Assaf Go
On Mon, Apr 4, 2011 at 5:55 PM, Kanwei Li wrote:
> Done the manual way
>
Thanks.
I was hoping to have finished this today, but it turns out there are
some subtle but annoying changes to how BLAST records the hit
id/name/description in their XML file which make the script to
convert from XML to t
Daniel,
Note that this (and similar) password solutions in Galaxy is not secure in any
real way (especially if you're dealing with patient data or HIPPA):
The password (hidden or visible in a text field) is still transmitted in
clear-text over the network (unless you're using HTTPS/SSL).
If you
Done the manual way
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Well, it could be modified to never return a value back to the
interface after being set. Would that be sufficient?
On Mon, Apr 4, 2011 at 11:46 AM, Daniel Schmidt wrote:
> Hello all!
>
> Thanks alot K! Although I have to admit, that it seems too insecure, at
> least for the tool I am currently w
On Mon, Apr 4, 2011 at 4:36 PM, Kanwei Li wrote:
> dhcp243253:galaxy-central kanwei$ hg transplant -s
> ~/peter/galaxy-central/ -b blast25
> searching for changes
> changeset: 5585:ab40f95393ec
> branch: blast25
> parent: 5583:086c9c2c52b9
> user: peterjc
> date: Mon Apr
Hello all!
Thanks alot K! Although I have to admit, that it seems too insecure, at
least for the tool I am currently working on. The password field is
needed to connect to a database, which contains (sensitive) patient
data. Revealing the password to someone else by accident when re-running
a
Hi,
We have a local mirror of the galaxy system and the disk is occupied really
quickly. Is there a way to purge histories/datasets not accessed/updated for
a certain period of time, no matter if they are deleted by the user? It looks
like the current scripts for clean up only purges deleted
dhcp243253:galaxy-central kanwei$ hg transplant -s
~/peter/galaxy-central/ -b blast25
searching for changes
changeset: 5585:ab40f95393ec
branch: blast25
parent: 5583:086c9c2c52b9
user:peterjc
date:Mon Apr 04 12:12:11 2011 +0100
summary: Update tests for NCBI BLAST 2
This fix got me further, however I'm now getting the following error, which is
now more confusing...
[bam_sort_core] merging from 40 files...
BGZF ERROR: unable to open file 1.0
BGZF ERROR: unable to open file 1.0
Could not open input BAM files
Juan
On Apr 1, 2011, at 1:53 PM, Dannon Baker wrot
Hi Sarah,
Does this occur with all histories? Does it change if you create a new
history?
--nate
Sarah Diehl wrote:
> Hi all,
>
> I encounter the same error that was already mentioned in this list
> (with the same email title). For me it also does only happen when
> debug is set to false. Howe
On Mon, Apr 4, 2011 at 4:10 PM, Kanwei Li wrote:
> I think it's because the parent of those changesets were before your
> merge, so the branches got messed up
But I haven't done any merge in this branch's history... It starts here,
with James' latest commit to the trunk:
https://bitbucket.org/ga
Joe,
I think all you have to do is set up auth in nginx (I use the http auth PAM
module in Linux from http://web.iti.upv.es/~sto/nginx/ configured based on the
accompanied documentation) and then tell it to set the REMOTE_USER variable
when it proxies for galaxy with (in location / or where app
Hi Daniel,
I have attached a patch that does this below. You can use it by
setting However the security is lacking as you
can see the string when you try to re-run the job and view source. Is
this sufficient for your purposes?
Thanks,
K
On Sat, Apr 2, 2011 at 11:01 AM, Daniel Schmidt wrote:
>
I think it's because the parent of those changesets were before your
merge, so the branches got messed up
On Mon, Apr 4, 2011 at 11:07 AM, Peter Cock wrote:
> On Mon, Apr 4, 2011 at 4:03 PM, Kanwei Li wrote:
>> I tried both ways, no dice (you can try yourself with a clean
>> galaxy-central base)
On Mon, Apr 4, 2011 at 4:03 PM, Kanwei Li wrote:
> I tried both ways, no dice (you can try yourself with a clean
> galaxy-central base)
I'm a bit puzzled and not an hg expert. Was there an error message?
And for plan (B), what went wrong with using patch and the raw
changes? Surely that should w
I tried both ways, no dice (you can try yourself with a clean
galaxy-central base)
On Mon, Apr 4, 2011 at 10:58 AM, Peter Cock wrote:
> On Mon, Apr 4, 2011 at 3:07 PM, Kanwei Li wrote:
>> Hi Peter,
>>
>> I think you need to merge your commits as I cannot seem to transplant
>> or import the patch
On Mon, Apr 4, 2011 at 3:07 PM, Kanwei Li wrote:
> Hi Peter,
>
> I think you need to merge your commits as I cannot seem to transplant
> or import the patches properly.
>
> K
Hi Kanwei,
I'm not sure why they won't transplant - they are both on this fresh
branch from the trunk, with just these tw
Hi Peter,
I think you need to merge your commits as I cannot seem to transplant
or import the patches properly.
K
On Mon, Apr 4, 2011 at 9:46 AM, Peter Cock wrote:
> On Mon, Apr 4, 2011 at 12:19 PM, Peter Cock wrote:
>> On Fri, Apr 1, 2011 at 12:01 PM, Peter Cock
>> wrote:
>>> On Thu, Mar 31
On Mon, Apr 4, 2011 at 12:19 PM, Peter Cock wrote:
> On Fri, Apr 1, 2011 at 12:01 PM, Peter Cock wrote:
>> On Thu, Mar 31, 2011 at 6:28 PM, Peter Cock
>> wrote:
>>> Hi all,
>>>
>>> The NCBI have just released BLAST 2.2.25+ which includes some
>>> interesting new stuff of interest to the tabular
On Fri, Apr 1, 2011 at 12:01 PM, Peter Cock wrote:
> On Thu, Mar 31, 2011 at 6:28 PM, Peter Cock wrote:
>> Hi all,
>>
>> The NCBI have just released BLAST 2.2.25+ which includes some
>> interesting new stuff of interest to the tabular output, ...
>
> One reason why I want to move to BLAST 2.2.25+
Hi,
We are getting multiple requests for this but did not have the
bandwidth to do it. So if you are planning to implement - share
through the toolshed and we will roll it to main.
The way I got round this was let the SRA website do the conversion. So just
paste in the URL in the upload s
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