-------- ???????? ????????? --------
????: deleting datasets from history
????: Tue, 5 Jul 2011 19:58:45 +0300
??: Sergei Ryazansky <s.ryazansky(a)gmail.com>
After the deleating datasets from the history panel in our Galaxy mirror
the indicator at the top right corner shows the same amount of used
space as before deleting. Also, the files corresponded to the datasets
remains in the Galaxy database/files/000 directory. It seems, that
deleting of datasets from history is only delete the launch to file but
not the file itself. How to configure the Galaxy mirror to delete not
only records in history panel but also the corresponed files?
Thank you in advance!
When I attempt to run cufflinks based on .sam output from bowtie I get an
An error occurred running this job: *cufflinks v1.0.1
cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.050000 -p 8 -b
Error running cufflinks. [Errno 2] No such file or directory:
*What can I do to get around this problem and run cufflinks?
My workflow is on http://main.g2.bx.psu.edu and can be found here (I ran it
using a .fastq file):
Thanks in advance for your help!
Lewis-Sigler Institute for Integrative Genomics
Carl Icahn Laboratory
I would like to generate a random intervals file by mimicking a bed file
of interest from the mouse genome.
Does someone know how to do that?
NB: the "random intervals" tool from "Encode tools" does this but only
for human genome.
referencing old thread:
is the delete functionality still status-quo? i.e - there is no delete other than the workaround?
switched from SQLlite to postgres and have this strange double login issue. Included image - need to login twice and logout twice. Double tab -
I am upgrading to the most recent galaxy-dist
First time run.sh shows following errors as in attachment.
It seems when I use 'manage_db.sh upgrade' it doesn't create necessary
tables for these tools.
Wonder if these are known issues?
I'm not familiar with Windows 7, so I'm forwarding your email to the galaxy public mailing list, where the Galaxy team can further help you with your fastq conversion.
Begin forwarded message:
Date: July 4, 2011 19:43:31 EDT
Subject: RE: uploading error
I followed the instructions you mentioned. I was able to upload the fastq file on the website.
However I am getting error while converting the fastq file to fasta format. I use windows 7.
> Date: Mon, 20 Jun 2011 14:18:31 -0400
> From: <mailto:email@example.com> gordon(a)cshl.edu<mailto:firstname.lastname@example.org>
> To: galaxy-user(a)bx.psu.edu<mailto:email@example.com>; <mailto:firstname.lastname@example.org> rdalvi01(a)students.poly.edu<mailto:email@example.com>
> Subject: Fwd: uploading error
> Hello Rubina,
> I've forwarding your email to the galaxy public mailing list, where the Galaxy team can further help you with your upload.
> Generally speaking, uploading big FASTQ using the web interface is prone to errors.
> The Galaxy team added a new upload method, using FTP, which is more reliable.
> Detailed instructions are available here:
> <https://bitbucket.org/galaxy/galaxy-central/wiki/UploadViaFTP> https://bitbucket.org/galaxy/galaxy-central/wiki/UploadViaFTP
> -------- Original Message --------
> Subject: uploading error
> Date: Mon, 20 Jun 2011 18:10:57 +0000
> From: <rdalvi01(a)students.poly.edu<mailto:firstname.lastname@example.org>>
> To: <gordon(a)cshl.edu<mailto:email@example.com>>
> My name is Rubina. I am using Galaxy to convert fastq files to fasta format.
> I tried to upload fastq file on the following link.
> <http://main.g2.bx.psu.edu/> http://main.g2.bx.psu.edu/
> However I am not able to upload. Its been a week, but it still shows uploading.
> Thank You,
First of all I would like to thank you guys for developing and mainting this
so useful tool as Galaxy!
I have our own installation fo Galaxy (galaxy-dist version) with
ncbi-blast-plus. Calling blastn results to the following error message:
An error occurred running this job:*Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/tools/ncbi_blast_plus/hide_stderr.py", line
29, in <module>
sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
NameError: name 'cmd' is not defined*
Could you please explain, what this error can mean?
The link to the shared history is* *
Thank you in advance!
I have a question for you guys regarding quality filtering.
I have a data set of double MID tagged 454 amplicons, from which I wish to
select high quality sequences above Q20.
The 454 quality filtering system seems to work differently from that given
for the Illumina sequencing i.e. 454 filtering takes high quality segments,
while Illumina (FASTQ) can select high quality full reads based on certain
OK, so I know that the total length of my amplicon, including primers and
barcodes is around 260bp. If I then set the 454 quality filtering tool to
extract contiguous high quality sequence of >260, it gives me back around
45% of my raw data as hitting this criterion i.e. All 260bp are above Q20. I
don¹t necessarily need this high stringency as most bases may not be
But if I convert my 454 data to FASTQ format and then run the Illumina
filtering system which also allows me to set the number of bases allowed to
deviate from the Q20 criteria, I get back over 90% of my data (allowing 10bp
to deviate from Q20).
I then need to go ahead and convert back to 454 format.
Can you tell me if this is OK?
Will I loose /confuse information somewhere along these conversions?
It seems that if I do this, my barcodes are removed, as amplicons do not
sort properly when I parse them through my barcode filtering program.
Does anyone know of a program to filter 454 data based on average sequence
quality score, which doesn¹t involve Linux and the Roche off instrument
program (I have no experience in Linux! )
Department of Biology,
Halifax, NS, B3H 4J1