Hi Greg,
what I mean is that I don't expect any other errors in my files since I
corrected the errors you reported. When using my XML editor I also don't get
any errors, so the files seem OK. However, the problem remains: one of the
tools and also the dependencies definitions don't appear in
Hi Arshad,
do you have samtools installed?
Galaxy will build an BAM index file automatically during upload, but
only if you have samtools installed.
Cheers,
Bjoern
I am trying to upload a bam file for my data analysis (size is about
9GB) I am trying URL method to up load and getting error
Hi Ira,
as far as I can see you missed the actions tag. That results in no log
message at all, since no action type is executed. Galaxy should probably
give an error here. Or better validate that during tool upload. I will
fill a Trello Card for it.
The following code snipped worked for me:
Ahhh ... Thanks .. I can't believe I missed that. Thanks for spotting it.
I'm not sure I understand enough about how this works to answer your ruby_home
question. Ill play with this more tomorrow and see how things work with my
tools and maybe have more feedback then
Cheers
Ira
On 29 Oct
Ahhh ... Thanks .. I can't believe I missed that. Thanks for spotting it.
No problem!
I'm not sure I understand enough about how this works to answer your
ruby_home question. Ill play with this more tomorrow and see how things work
with my tools and maybe have more feedback then
Sure,
On Tue, Oct 29, 2013 at 6:23 AM, Lukasse, Pieter pieter.luka...@wur.nl wrote:
Hi Greg,
what I mean is that I don't expect any other errors in my files since I
corrected the errors you reported. When using my XML editor I also
don't get any errors, so the files seem OK. However, the problem
Hi Pieter,
The tool shed is undoubtedly not the problem here. The tool is simply not
identified as a Galaxy tool for some reason. When it had xml validation
errors, it was not loaded as a Galaxy tool due to the errors. I'm not sure
what new issue is causing the xml to not load properly as a
Whoever your organization administrator is will need to either create those
keys for you, or allow your IAM user access to them. Are you able to
contact the person that administers your account?
On Tue, Oct 29, 2013 at 10:52 AM, Manisha Sapre msa...@nmdp.org wrote:
Good Morning Dannon
we
Jennifer,
What's the status of bowtie2/mm9 index on PSU main?
When I select tophat2, it offers me mm9 as a choice for built-in indexes.
However, when the job runs, I get the following error, indicating the
bowtie2/mm9 indexes are missing (below).
Any insight into whether this is expected, or
Maybe I misunderstand what you're trying to do, but you shouldn't have to
use ssh-add or anything of the sort; cloudlaunch will do this for you.
When you put your credentials into those two boxes at
usegalaxy.org/cloudlaunch, what exactly happens?
On Tue, Oct 29, 2013 at 11:21 AM, Manisha Sapre
Hi Kyle,
Swift indeed is a complete framework for distributed computing.
Distributing files out to cluster nodes, starting processes, bringing back
result files to submit host is done out of the box (stagein-exec-stageout
cycle).
We can discuss offline if you are interested in giving it a shot.
Your ssh keys are completely different from the keys you're looking for
here. An AWS account with root access should be able to see these, as far
as I know, but since you're unable to see them for whatever reason you will
need to contact the primary administrator for your AWS account and I'm sure
I am having an issue trying to do anything. I click on a tool, the screen pops
up in the middle but then when I move my mouse over to that screen, the drop
down menus all pull down in a large black screen so that I cannot get to
anything. The screen also does not go away if I try to click away
Greetings-
I tried to run an alignment using Bowtie2 and got this message-
format: bam, database: mm9
Could not locate a Bowtie index corresponding to basename
/galaxy/data/mm9/mm9canon/bowtie2_index/mm9canon Error: Encountered internal
Bowtie 2 exception (#1) Command:
Is this a local galaxy setup that you host ... or the public one?
It sounds like a cache issue on your end (clear your browsers cache).
If this is a local setup that you host, perhaps you are not loading
CSS/javascript? Are those being blocked? Are you running a reverse
proxy? Have the redirects
Alan,
At first glance this look promising. I am a little leery of tools that claim
to do parallel processing. However I would like to test it out on our HPC
cluster here at UCI.
Few questions:
Could you explain how your tool actually does the parallel processing on
something that is sequential?
Hi Greg,
do you mean that patch?
https://bitbucket.org/galaxy/galaxy-central/commits/all?search=83bed9c7dbbc
I can reproduce that error and it is not fixed with latest
galaxy-central, or did you only applied it to next-stable?
You can test with my augustus repository if you like.
hi Adam,
Could you explain how your tool actually does the parallel processing on
something that is sequential? For example in your PDF you mention the fastq
example, but I do not see the explanation as to how it splits up the work
across multiple cores/nodes. Does it simply split the
Hi Bjoern,
Changing the title to reflect the proper topic
I see now that the gem executables are installed under $INSTALLDIR/bin so I
added this to the environment for my protk install.
That got me to the point where my executable would run ... but now I'm seeing
that in my env.sh file I
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