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
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+
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
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 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
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 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 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)
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:
>
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
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
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
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
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
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
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
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
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
Done the manual way
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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
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
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
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