A researcher here was trying to use Galaxy Picard sam2fastq tool to generate a single fastq file from a sam file that has a mix of paired and unpaired data. She was thinking the second input on the sheet might control this:
> Do you want to output a fastq file per read group (two fastq files per read group if the group is paired)
> OUTPUT_PER_RG; default=False
But preliminary testing indicates there is no output scenario that includes both paired and unpaired data in the output (esp. as just one file). I just wanted to verify that this was the case, since the docs don't talk about this scenario? We're planning instead to write a little Galaxy tool that does what she gets accomplished on the command line:
> samtools view -bS in.sam > out.bam
> bamtools convert -format fastq -in in.bam > out.fastq
which includes unpaired reads too.
Thanks for feedback,
Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control
655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
I’ve had a report from my users that the count.seqs function in Mothur doesn’t work and just produces an empty table - this is also what I’m seeing when testing it both on the current July 2015 distribution, plus I went back to my backup server still running the May 2015 version.
I’ve attached a test set and using the latest Mothur installation and running count.seqs on this seems to work according to the logs but the output file is empty. Datatype needs to be set to names when this is imported of course. I would like to get this working because at the moment my users have to go back to the CLI version to do their work.
Dr. Shane Sturrock
NZGL BioIT Admin
I am developing a tool for biologists, I managed to integrate it with
Galaxy (it's a KNIME/R-based machine learning workflow).
This tool doesn't require a lot of interaction from the user - just a list
of IDs pasted-in and maybe 1-2 text entry fields - then it's just Execute.
Even though the inner works of Galaxy are great and I got a grip of it, we
believe that for our needs the workflow-based system with a tool and data
list is a bit confusing for non-computational people who don't want to
spend too much time on learning the interface (I know it's not complicated,
but we know how people are...).
So what we're aiming for is to put some sort of Google Search-like front,
as simple as possible. Could anyone point me in the right direction, how to
do it ? Or maybe anyone ever did something like this ? I could imagine that
it should be easy, since we want to remove almost all elements, not write
them from scratch.
Any ideas ?
I have encountered the following issue when I try to use FastQC tool in Galaxy. The fastqc file is validated using the fastqvalidator tool and the same files have been processed by other tools (i.e bwa) without any complaints about the fastqc . Also, if I ran the fastqc from the command line it gets executed without any issue too.
I have updated my galaxy repository in case there is new updates and the FastQC version is v0.11.2
Is this something to do with the FastQC wrapper in galaxy?
If it helps, the fastq files are in the file system and I link to them into galaxy using the options Link and Fastqqsanger as data type.
Any help will be highly appreciated.
Fatal error: Exit code 1 ()
Failed to process L-20417_S7_L007_R2_001.fastq
uk.ac.babraham.FastQC.Sequence.SequenceFormatException: ID line didn't start with '@'
Traceback (most recent call last):
File "/gpfs/home/galaxyadmin/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/8c650f7f76e9/fastqc/rgFastQC.py", line 162, in <module>
File "/gpfs/home/galaxyadmin/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/8c650f7f76e9/fastqc/rgFastQC.py", line 136, in run_fastqc
File "/gpfs/home/galaxyadmin/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/8c650f7f76e9/fastqc/rgFastQC.py", line 109, in copy_output_file_to_dataset
with open(result_file, 'rb') as fsrc:
IndexError: list index out of range
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The Galaxy Community Conference has been held annually since 2010. GCC2016
<http://galaxyproject.org/GCC2016> will be held June 25-29 at Indiana
University <http://indiana.edu/> in Bloomington, Indiana, United States.
*We are now seeking proposals
organizations interested in hosting GCC2017.*
Galaxy's informal policy of rotating between North America and elsewhere
every other year is now a formal policy: Hosts for GCC2017 need to be
located outside of North America.
GCC draws 200+ participants from data-intensive life science research.
Participants come from around the world, from all career stages, and do
research spanning the tree of life. Universities, hospitals and medical
schools, research organizations, and industry are all represented,
including some of the largest and most influential research organizations
in the world.
What do you need to host GCC2017, you ask? In approximately decreasing
order of importance:
*Enthusiasm to plan and organize several events over 5 days for more
than 200 people.*
- Space for 4-6 parallel training sessions over two full days, with each
space able to accommodate 25 to 75 participants.
- Central meeting space with capacity for 250-300 people.
- Affordability (or access to sponsorship funds; there's a reason we've
always held GCC in academic settings)
- Nearby space for breakouts, poster sessions and sponsors.
- Nearby space for lunch, coffee breaks.
- Good wifi for all events (that's 200+ people and their devices).
- Space for hackathons for 2 days before the event.
- Easy to get to by air.
- Nearby, affordable housing, or easy walking distance or easy public
transport from lodging options to conference facilities
- Close proximity to a pub and other social hubs.
Hosts get copious (and enthusiastic) organizational support from Galaxy's
Outreach Team (who have been helping to organize GCC since 2011), and even
more copious gratitude (even *adulation!)* from the Galaxy Community.
See the *full call for host proposals
more details on what should be covered in proposals. Proposals are due by
the end of 30 October 2015. If you are interested in possibly hosting
GCC2017 then please contact Galaxy Outreach <outreach(a)galaxyproject.org> with
any questions. Our goal is to announce GCC2017 at GCC2016 this coming June.
Hoping to work with you in 2017!
Dave Clements and the Galaxy Team
The LWR has been deprecated for over a year now. It has been renamed
and replaced by Pulsar which has many advantages over the previous LWR
code base. Instructions on migrating from the LWR to Pulsar can be
found here - http://pulsar.readthedocs.org/en/latest/upgrading.html.
There have been several great efforts to cleanup the Galaxy codebase
lately and I think it may be time to remove legacy LWR support to help
with these. Would there be any objections to removing LWR support from
Galaxy with say release 15.10 next month?
I would like to open a Galaxy session programmatically (schedule Galaxy with their user name and password) and have the Galaxy session open with a history name I specify. So if there was work done previously under that history name, those output files will appear in the history window -- without the user having to change the history name manually to see them.
Is this possible?
I have a script that is 'running' according to galaxy but it never
completes. When i looked in the terminal, the processes were stuck in
a Unix 'T' state, which means they're of course never going to finish.
Is galaxy causing these scripts to go into a T state or is the problem
somewhere else? I'm at a loss
Dear Galaxy devs / support,
I am trying to understand the following snippet from job_conf.xml (I
want to use drmaa v1)
<destination id="pbs_drmaa_orion" runner="drmaa" tags="merc">
Based on someone's configuration above, I am trying to customize to my
I'm trying to understand where/how the parameters are associated?
- destination in param id? is this the queue? I also checked the DRMAA
specification but cannot find any "destination" as a keyword.
- galaxy@merc? is merc pointing to the hostname, and galaxy the queue
name? (I know the instution's cluster is called "merc", but I don't know
if the "merc" in the tag is for convenience or is being read as the
I've looked through:
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServerhttps://wiki.galaxyproject.org/Admin/Config/Performance/Clusterhttps://wiki.galaxyproject.org/Admin/Config/Jobs - describes job_conf.xml
but cannot make sense, eg. for "tags" is says "Tags to which this
Do you have more detailed documention on configuration?
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