setting environment for sge scripts
by Andreas Kuntzagk
Hi,
I followed the advice for multiple installed python versions to set
~galaxy/galaxy-python/python and set the environment for the galaxy user
to have that in the PATH
Problem is, when a job is started on GridEngine, it does not use the
"-V" flag to inherit the environment. So it runs with a different python
version and more important it does not set LD_LIBRARY_PATH and fails for
some tools which need some special lib. (libRblas in this case)
Where can I fix that?
regards, Andreas
11 years, 3 months
Small RNA gene, tRNA genes
by Kluger, Yuval
Hi,
I would appreciate any suggestion how one can use Galaxy to obtain coordinates of human and mouse of all known tRNAs.
Similarly how one can do that for other types such as miRNAs and other small RNAs .
Thanks,
Yuval
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11 years, 4 months
eprimer3 missing?
by Erick Antezana
Hi,
I have seen that many tools from EMBOSS have already an "XML tool
file" (.../tools/emboss_5/*.xml). I couldn't find the one for eprimer3
(it seems it was there before? as it could be seen in
./.hg/store/fncache : data/tools/emboss/emboss_eprimer3.xml). I
have looked for it in the bitbucket but I couldn't find it... Has it
ever existed? or should I create myself an XML for such tool?
cheers,
Erick
11 years, 5 months
Maq output
by Michaela Lee
Does anyone know if Maq can produce alignment data in SAM format? Currently
we can only generate outputs in fastq format. Is there a way Galaxy can
convert a fastq file to a SAM file? I did not see it as an option but I
thought I'd ask. Thanks!
Michaela
11 years, 5 months
pysam egg
by Erick Antezana
Hi,
I've just updated my Galaxy install. Everything works fine. I only had
an issue while trying to use the pysam egg. The error message is the
following:
ImportError: /lib64/libc.so.6: version `GLIBC_2.7' not found (required
by /home/bio/erick/.python-eggs/pysam-0.1.1-py2.4-linux-x86_64.egg-tmp/pysam/csamtools.so)
Unfortunately, we have in our system GLIBC 2.5 (glibc-2.5-42.el5_4.2).
We have tried to bypass such requirement by compiling pysam and
manually copying the csamtools.so file without success. Once I try to
launch Galaxy (run.sh) it fetches the original egg (and so library)...
The variable FETCH_EGGS was set to 0 but it is still fetching the
latest versions...Are we missing something? Otherwise, would it be
possible to have such egg for glib 2.5 ?
thanks,
Erick
11 years, 5 months
Re: [galaxy-user] GALAXY Question
by Guruprasad Ananda
Hi Mike,
Do you mind sharing your history with me (guru(a)psu.edu) so that I can take a look at what might be going on?
Thanks,
Guru.
> From: Michael Wilson <michael.d.wilson(a)gmail.com>
> Date: January 26, 2010 12:43:30 PM EST
> To: Anton Nekrutenko <anton(a)bx.psu.edu>
> Subject: Re: [galaxy-user] GALAXY Question
>
> Dear Anton,
>
> I have a question regarding the 'Base Coverage' function. I have a 9 column interval file and when I perform 'Base coverage' it reports 0 bp of sequence despite there being many intervals. If I convert the same file to a bed file and then perform 'Base Coverage' I get the correct number of basepairs. There does not seem to be any problem with my interval files. I was wondering if this may be a bug.
>
> As I would like to use 'Base Coverage' in one of my workflows I tried to get around this problem by converting my interval files to bedfiles with 1:chrom 2:start 3:end (I do not indicate strand or name in these bedfiles). However when I use Filter and Sort: Select > ^chr21 , the new bedfile which is created with only lines starting with chr21 has for some reason had column 6 replaced with '+' and is labelled as 'strand' and column 8 is labeled with 'name'. I am not sure why the bedfile changes format after using the select command and if this is intentional or if you know a way around this happening.
>
> 1) can you use Base Coverage on interval files?
> 2) is there a way to avoid changing the column designations in a bedfile when using Filter and Sort: select.
>
>
> Thank you again for all your help and excellent resources.
>
> Best regards,
>
> Mike
11 years, 5 months
Re: [galaxy-user] [galaxy-bugs] workflow database
by Jeremy Goecks
Hi Jason,
In the last couple weeks we've written the infrastructure that (a) enables users to publish workflows and (b) provides a way to browse, search, view, and use published workflows. (Histories and pages will have the same functionality as well.) This code is making it's way to our main webserver (it's being tested right now), and it should become available within the week.
FYI, the links for published items will be:
http://main.g2.bx.psu.edu/workflow/list_published
http://main.g2.bx.psu.edu/history/list_published
http://main.g2.bx.psu.edu/page/list_published
Finally, a good place to pose these types of questions is galaxy-user, which I've CC'ed
Best,
J.
On Jan 24, 2010, at 3:18 PM, Jason Miller wrote:
> Hi I'm a user of galaxy and I was wondering if there is a database or website where users can submit workflows to be public? I know it's possible to make links or share with other users, but I thought it would be a good idea to have a database of workflows for everyone to see.
> Thanks
> Jason
>
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
> galaxy-bugs mailing list
> galaxy-bugs(a)lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-bugs
11 years, 5 months
Re: [galaxy-user] alignment question
by Anton Nekrutenko
Michaela:
Sorry for delay in replying. Looks like you need to do this:
1. Map reads with bowtie using "try hard" option.
2. Leave -m option at -1
3. Set -k ridiculously high (e.g., 1000)
4. Once mapped filter SAM with "SAM Tools->Filter SAM on bitwise flag"
filter tool using option as in the attached image
5. Convert SAM format to intervals using "Covert SAM to interval" tool.
6. Subtract coordinates of regions from the previous step from
coordinates of your exons using "Operate on Genome Intervals-
>Subtract" tool. The result will contain unmapped regions.
Let me know how it goes, and always cope to galaxy-user mailing list.
Thanks,
anton
galaxy team
On Jan 20, 2010, at 2:16 PM, Michaela Lee wrote:
> Hi Anton,
>
> I am sorry to keep bothering you but could you clarify a bit more on
> what I can do with mapped reads on Galaxy? Here is my situation:
> We have attempted to sequence all the exons on the X chromosome for
> some of our subjects through exon capture and high through-put
> sequencing. We have all the Illumina reads on an external hard
> drive and would like to know which regions of our reference sequence
> were not "captured" or sequenced after mapping all the reads using
> Maq or Bowtie. We are not interested in unmapped reads, just the
> unmapped regions of the reference sequence.
>
> I have watched video #7 of Galaxy but I am confused as to which
> "bitwise flag" I would use to have Galaxy generate an output file
> with a list of regions of the reference sequence that were not
> mapped. Ultimately, we would like to compare all the regions that
> were not captured for all our subjects to see if those unsequenced
> regions are random or not.
>
> I appreciate any help you can give me. Thank you!
>
> Michaela
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
11 years, 6 months
Sharing Histories, Workflows, and Pages
by Jeremy Goecks
Hi all,
Changeset 3253 stabilizes Galaxy's item sharing; items that can be shared
are histories, workflows, and pages. There are now three types of sharing
for items:
(1) sharing via email with other users (unchanged);
(2) making an item accessible via link (similar to 'enable import via
link'); and
(3) publishing an item.
Sharing via email is unchanged; you can share item with individual users by
specifying their email addresses.
Making an item accessible via link generates a human-readable link that can
be shared with other people; via this link, users can view or import an
item. Publishing an item makes the item accessible via link and lists the
item's link in Galaxy's public repository so that anyone via browse or
search for it.
Hence, in reference to a previous discussion about item sharing, it is now
possible to generate a link for accessing an item but not publish the item's
link.
This changeset is available now in our development repository and will make
its way to our dist repository and our main server in the next week.
Comments, questions, and suggestions are welcome.
Thanks,
J.
11 years, 6 months
alignment question
by Michaela Lee
Hello,
I was wondering if Galaxy can align Solexa reads to a reference sequence.
If not, can I upload my alignment data from Maq onto Galaxy and somehow work
with that data online? Also, can Galaxy tell me which parts of the
reference sequence have no reads aligned to them? I am basically trying to
figure out which parts were not sequenced and compare those sequences
between different subjects.
Thanks for your help.
M
11 years, 6 months
