We recently installed NCBI BLAST + to our local Galaxy instance and now we need to provide the possibility to filter/mask ... by taxon id (taxid) using the command line option (-window_masker_taxid) of BLAST (cf. http://www.ncbi.nlm.nih.gov/books/NBK1763/) before the job will be performed in one task.
However searching in the documentation and the mailing list, I did not find anything about this.
So it would be great to provide the possibility to subselect by taxid (e.g. NCBI BLAST server http://blast.ncbi.nlm.nih.gov/Blast.cgi) by changing the BLAST integration.
We believe this could be of common interest. It would be great if anybody could comment on this.
Thanks a lot, Thomas
Is there a default notation to specify perl modules (threading modules)
in a tool configuration or in a submission to the toolshed?
I've got some tools to share that make extensive use of these modules,
and they are not default in a perl distribution. Hence, I'd like to
inform the users that they need to install these modules (or that they
get installed by the the toolshed using cpan ?)
Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
Tel: +32 (0)3 275 97 56
I have several jobs have been stuck in the queue for long time, I checked
the handler log and found the following message:
Job runner assigned but no external ID recorded, adding to the job handler
Is there a way that I can clean these orphan jobs out of the queue?
After installing the BWA from the Tools Shed, I find there is a
new tool_data_table_conf.xml got created under tool-data directory. The
file contains the entries of BWA's loc files.
I believe the installed BWA still relies on the tool_data_table_conf.xml
under galaxy root dir. Anyone can clarify what the one under tool-data dir
I have managed to get proftpd to work, it can connect to the galaxy sql database, and users can log to upload files in their directory. But there is a problem, when a galaxy user logs in the galaxy web platform, the user can't see his upload files since Galaxy doesn't have the rights to open the directory. How can i change the permissions in proftpd so that galaxy can open the user directory?
Thanks in advance to all.
What is the current status in Galaxy for supporting compressed files?
We've talked about this before, for example in addition to FASTQ,
many of us have expressed a wish to work with gzipped FASTQ.
I understand that some have customized their local Galaxy
installations to use gzipped FASTQ as a specific data type - I'm
more interested in a general file format neutral solution.
Also, I'd like to be able to used BGZF (not just GZIP) because it
is better for random access - see for example
- and makes it much easier to break up large datafiles for sharing
over a cluster (i.e. it could be exploited in the current Galaxy code
for splitting large sequence files).
The 11 May 2012 Galaxy Development News Brief
mentions tabix indexing - that uses bgzip, so is there something
general in place yet to allow tool wrappers to say they accept not just
given file formats, but different compressed versions of file formats?
Ideally I'd like to be able to write an XML tool description saying
a tool produced BGZF compressed tabular data, or GZIP
compressed Sanger FASTQ etc. Similarly, I'd like to specify my
tool accepts FASTA or gzipped FASTA (including BGZF FASTA).
While for older tools if they say they accept only uncompressed
FASTA, Galaxy could automatically decompress any compressed
FASTA entries in my history on demand.
I would like to inquire whether anyone has attempted to implement the
idxstats tool from samtools into Galaxy?
The xml-file for idxstats is not present in the Galaxy source code,
which led me to try and implement it myself.
However, the main problem I face is that the idxstats tool silently
relies on having an index file available (within the same directory)
for the bam file you which to print the stats for.
samtools idxstats PATH/test.bam
searches for PATH/test.bam.bai and gives an error when this file is not
present. And somehow I cannot model this behavior in Galaxy.
A different solution would of course be to ask the author(s) of samtools
to have an option available where the user can directly indicate the
path to the index file.
PS: I've searched the mailing list archives for this problem but did not
find any matches. Apologies if I somehow missed the answer.
Michiel Van Bel, PhD
Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
I'd like to be able to write some simple <test> entries for
some of the BLAST+ tools using composite datatypes
as input or output (i.e. small BLAST databases). This
doesn't seem to be mentioned or hinted at on the wiki:
Is it possible to use a composite datatype as a test input?
If so how? Normal datatypes are loaded into the test history
using using the upload tool - does that mean I first need to
extend the relevant datatypes to allow them to be uploaded?
Example: Run blastp using a small query FASTA file and
a small database, check the output (eg tabular).
Is it possible to use a composite datatype as a test output?
If so how?
Example: Run makeblastdb using a small FASTA file, and
check the output (a small BLAST database).
I apologize for the delay, here is the information you requested:
ubuntu@ip-10-0-0-243:~$ uname -a
Linux ip-10-0-0-243 3.8.0-25-generic #37-Ubuntu SMP Thu Jun 6 20:47:07
UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
ubuntu@ip-10-0-0-243:~$ echo $0
On 08/26/2013 09:44 AM, Peter Cock wrote:
> (Off list)
> Hi Dave, Greg,
> Just a reminder - without a bit more information about the Tool Shed
> cluster I am stuck about how to debug this install issue.
> On Wed, Aug 21, 2013 at 2:05 PM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
>> On Wed, Aug 21, 2013 at 1:45 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
>>> Here is the relevant log output for the installation of ncbi_blast_plus. A
>>> quick google informs me that exit code 64 means "command line usage error",
>>> for what it's worth.
>>> tool_shed.util.shed_util_common DEBUG 2013-08-20 23:34:47,886 Adding new row
>>> (or updating an existing row) for repository 'package_blast_plus_2_2_26' in
>>> the tool_shed_repository table, status set to 'New'.
>>> Warning: local() encountered an error (return code 64) while executing '
>>> if [[ "$(uname)" == "Linux" ]]; then export
>>> FILENAME="ncbi-blast-2.2.26+-ia32-linux.tar.gz"; fi &&
>>> if [[ "$(arch)" == "x86_64" ]]; then export
>>> FILENAME="ncbi-blast-2.2.26+-x64-linux.tar.gz"; fi &&
>>> if [[ "$(uname)" == "Darwin" ]]; then export
>>> FILENAME="ncbi-blast-2.2.26+-universal-macosx.tar.gz"; fi &&
>>> echo Fetching $FILENAME &&
>>> if [[ "$(uname)" == "Linux" ]]; then wget
>>> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi &&
>>> if [[ "$(uname)" == "Darwin" ]]; then curl -O
>>> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi &&
>>> tar -zxvf $FILENAME &&
>>> echo Downloaded and decompressed
>> Thanks Dave,
>> I've made a note on this Trello card about exposing the log information
>> of unsuccessful builds on the Tool Shed,
>> Can you tell me what version of Linux this is, and which shell?
>> $ uname
>> $ arch
>> $ echo $0
>> That might give me a clue about the nature of the failure. My
>> hunch is that I am using something bash specific.
>> The simplest solution would be if you could run each of these
>> command by hand to see if it triggers the same error:
>> if [[ "$(uname)" == "Linux" ]]; then export FILENAME="ncbi-blast-2.2.26+-ia32-linux.tar.gz"; fi
>> if [[ "$(arch)" == "x86_64" ]]; then export FILENAME="ncbi-blast-2.2.26+-x64-linux.tar.gz"; fi
>> if [[ "$(uname)" == "Darwin" ]]; then export FILENAME="ncbi-blast-2.2.26+-universal-macosx.tar.gz"; fi
>> echo Fetching $FILENAME
>> if [[ "$(uname)" == "Linux" ]]; then wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi
>> if [[ "$(uname)" == "Darwin" ]]; then curl -O ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi
>> tar -zxvf $FILENAME
>> echo Downloaded and decompressed