Velvetoptimiser error
by Makis Ladoukakis
Dear Galaxy users,
Has anyone worked with velvetoptimiser tool from the Tool shed?
I have been trying both the stable and the test version of the velvetoptimiser tool and i keep getting the same error:
Traceback (most recent call last):
File "/home/ladoukef/galaxy_dist/tools/myTools/velvetoptimiser/velvet_optimiser.py", line 102, in
if __name__ == "__main__": __main__()
File "/home/ladoukef/galaxy_dist/tools/myTools/velvetoptimiser/velvet_optimiser.py", line 67, in __main__
for line in open(contigs_path ):
IOError: [Errno 2] No such file or directory: 'contigs.fa'
Can someone identify where the error is? The file missing (contigs.fa) is supposed to be built by the tool itself.
Thank you,
Efthymios Ladoukakis
9 years, 9 months
Workflows & Multiple datasets
by Adhemar
Hi,
I was searching for how to run a workflow for multiple input files and I
was very happy to find it's already implemented as mentioned here:
http://wiki.g2.bx.psu.edu/News%20Briefs/2011_05_20
The problem is that it's not working for me. When I select two files, for
example, it runs the workflow only in the first file. Even if I check 'Send
results to a new history', it only creates a new history called 'test 1'
and not the others. Is my instance somehow misconfigured or it's happening
to others as well?
I'm also looking for a way to add datasets to a library from different
histories. Do I really need to open each history one by one and use 'Import
datasets from your current library'?
Thank you,
Adhemar
9 years, 9 months
Tophat jobs not starting
by Magdalena Strzelecka
Hi,
I have submitted some jobs to Tophat, but they have not started since
yesterday (Dec 13th); i.e they were in a queue for >12 hrs. I have re-
submitted everything again (2 jobs), but the same situation is
happening. Is there some issue with Tophat at the moment?
Thanks.
M.
------------------------------
Magdalena Strzelecka, PhD
Heald Lab
University of California, Berkeley
Department of Molecular & Cell Biology
315 Life Sciences Addition # 3200
Berkeley, CA 94720-3200
phone: (510) 643-5002
fax: (510) 643-6791
e-mail: strzelecka(a)berkeley.edu
9 years, 9 months
Finding Galaxy version
by Paul-Michael Agapow
A perhaps obvious question: how do I work out what version of Galaxy an
instance is?
This has come up a few times because of apparent bugs and different
behaviour across various development and production instances. Now if
you're installed straight from the repo, you can use "hg log" for the
repo number. But that doesn't work if it's been installed in another
way, say from a tarball or via another versioning system (we use git to
synchronize tool development to a production server).
Simple solution?
----
Paul Agapow (paul-michael.agapow(a)hpa.org.uk)
Bioinformatics, Health Protection Agency
-----------------------------------------
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9 years, 9 months
comparing data sets with different coordinates
by dvera＠bio.fsu.edu
Hello,
May I use galaxy to do correlation analyses with two continuous
quantitative data sets containing different coordinates (two different
microarray designs)?
How can I create sliding windowed averages for these data sets to
accomplish this?
How can I perform a correlation analysis with a wiggle and a bed (e.g.,
microarray data VS gene density).
Would I need to do a grouping of my microarray data with another
spreadsheet defining the window coordinates?
Thanks,
Dan
9 years, 9 months
Performing operations on tab delimited text files
by Lanelle Oni Edwards
Hi,
My name is Lanelle Edwards. I am a new galaxy user. I uploaded a tab delimited text file to my history. However, the first column of the data I imported is solely chromosome number and start and end position (ALL IN ONE COLUMN) in the format chrI:1000000-2000000. My question is: How can I filter out these values into separate columns using galaxy tools? For example: Having a separate column for chromosome number, column for start position, column for end position. I would really appreciate the help.
Thanks,
Lanelle Edwards
Lab Manger
University of Maryland
9 years, 9 months
(no subject)
by Giuseppe Petrosino
Hi,
I read on Readme for MACS that: "For the experiment with several
replicates, it is recommended to concatenate several ChIP-seq treatment
files into a single file".
Now, I have illumina ChipSeq data: two files for IP samples and two files
for Control samples. Is It right to use Concatenate datasets (text
manipulation) and then use MACS for the peaks calling?
Thank you so much.
Giuseppe
9 years, 9 months
about ftp setting up
by Liao_Ruiqi
Hello there，
I'm a student at Fudan University in China. I was trying to enable ftp uploading in my local version of GALAXY.
I tried the setting in http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP, but I got the following problems:
1. The galaxyftp seems to be a pasql database, shall I build it myself? or dose it already exists in galaxy directory?
2. the galaxy_user seems to be a table, shall I build it myself? and how shall I update it and integrate it with galaxy?
Thanks for your attention, and looking forward to your reply!
Best wishes
Liao Ruiqi
9 years, 9 months
Extract genomic DNA
by Rebecca C Mueller
Hi all,
Does anyone know if you can use the "Extract Genomic DNA" command with
a genome not in the database? I am working with an algal genome (C.
merolae) that isn't currently in the pulldown Database/Build menu. I
keep getting the "Unspecified genome build" error, and am assuming
that's the problem, as my other files appear to be formatted correctly
(tab delimited without spaces for the intervals, same names for
chromosomes in interval and fasta file, etc).
Thanks!
Rebecca
9 years, 9 months
Looking for Galaxy related papers (or have written one)? There is a new Galaxy Group @ CiteULike
by Dave Clements
Hello all,
A new Galaxy Group
<http://www.citeulike.org/group/16008/order/group_rating>has been
created at the
CiteULike <http://citeulike.org/> social bookmarking service to organize
papers that are about, use, or reference Galaxy. The Galaxy
Group<http://www.citeulike.org/group/16008/order/group_rating>is open
to any CiteULike user (and anyone can become a CiteULike user).
Group members can add papers to the group, assign tags, and rate papers.
CiteULike makes extensive use of *tags* to organize and categorize papers.
The Galaxy group uses this set of
tags<http://wiki.g2.bx.psu.edu/CiteULike#CiteULike_Tags>to categorize
papers. If you want to help other Galaxy users and sites
find papers that are relevant to them, or help the Galaxy Project keep
track of what papers (and communities) are using Gaalxy, then please help
by adding relevant papers to the Galaxy Group
Library<http://www.citeulike.org/group/16008/order/group_rating>and/or
rating and tagging the papers that are there.
*We particularly need help with papers that were published before this
year, as very few of them are in the initial list. *
Links:
http:/galaxyproject.org/wiki/CiteULike - Explanation of tags
http://www.citeulike.org/group/16008/order/group_rating - Galaxy Group
list of papers
Thanks,
Dave Clements
PS: To cite the Galaxy Project, see
http://galaxyproject.org/wiki/Citing%20Galaxy.
--
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
http://galaxyproject.org/wiki/
9 years, 9 months
