Hello,
Has anybody written a mosaik reference-alignment/assembly tool for galaxy that
they would be willing to share?
Thanks,
Isabelle
--
Isabelle Phan, DPhil
Seattle Biomedical Research Institute
+1(206)256 7113
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galaxy-dev mailing list
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I would like to propose adding a "format_source" attribute to the tool_config
output data element.
This would be a backward compatible change. It is analogous to the
"metadata_source" attribute.
Motivation:
It is often convenient to have an output dataset inherit the format of an
input dat
I have a tool that takes a pair of files and manipulates them and produces a
new pair of files. One output file corresponds to the first input file, the
second output file corresponds to the second input file. I would like to label
them as such. Right now I get two datasets in the history tha
We've created a Galaxy development mailing list to go along with the Galaxy
development site. This mailing list will be used for communicating changes and
questions about developing for Galaxy on the Helix Systems. Not everyone is on
it, only those who specifically requested for access. If yo
John Powell (NIH/CIT) [E] wrote:
>
> Trying to install a local copy of Galaxy for evaluation. Downloaded
> the "stable" version using:
>
> hg clone https://bitbucket.org/galaxy/galaxy-dist
>
> I am installing it on a Centos 5 x86_64 Linux kernel which has
> python 2.4.3 installed. When running
Trying to install a local copy of Galaxy for evaluation. Downloaded
the "stable" version using:
hg clone https://bitbucket.org/galaxy/galaxy-dist
I am installing it on a Centos 5 x86_64 Linux kernel which has python
2.4.3 installed. When running "sh setup.sh" the installation stops
with a
My thanks as well, since we don't really have a way to debug LSF here.
Platform only granted us a 1 month license for the development, so I'd
have to get another license to debug it.
--nate
Leandro Hermida wrote:
> Hi Marina,
>
> Thanks for posting updates and information... we've moved from SGE
On 02/08/2011 12:50 PM, Kempenaar, M (med) wrote:
Hello Hans-Rudolf,
Do you know if the 'dynamic_options' attribute also works for control elements
other then select menu's?
For example I want to present the user a set of checkboxes that correspond to
column names from a file, could I use so
Hello Hans-Rudolf,
Do you know if the 'dynamic_options' attribute also works for control elements
other then select menu's?
For example I want to present the user a set of checkboxes that correspond to
column names from a file, could I use something like a loop that either
iterates on data rece
On Tue, Feb 8, 2011 at 8:15 AM, Kevin Lam wrote:
> Have you looked at
> http://code.google.com/p/cutadapt/
> Features
>
> Gapped alignment with mismatches and indels, that is, errors in the adapter
> are tolerated
> Finds adapters both in the 5' and 3' ends of reads
> Accepts FASTQ, FASTA or .csfa
On Tue, Feb 8, 2011 at 3:46 AM, Jennifer Jackson wrote:
> Hello Peter,
>
> If these are standard length PCR primers, then UCSC's In-Silico PCR tool
> would be an option. It is a varient of BLAT and the source is available from
> Kent Informatics. Here is a UCSC link to the online version (send Jim
Leandro
we use the "dynamic_options" attribute, eg:
and then we have a little python script ("extra_code_for_foo_list.py")
with the "ds_fooOptions" function, eg
def ds_fooOptions():
"""List available foos as tuples of (displayName,value)"""
foo
Have you looked at
http://code.google.com/p/cutadapt/
Features
- Gapped alignment with mismatches and indels, that is, errors in the
adapter are tolerated
- Finds adapters both in the 5' and 3' ends of reads
- Accepts FASTQ, FASTA or .csfasta and .qual files (for AB SOLiD data)
- An
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