Thanks for the quick answer. Could access bowtie2 from command line without a problem. Found that I had to include a line pointing to the wrapper in tool_conf.xml. It wasn't there by default. Now two new problems:

- bowtie2 does not show any built-in reference genomes

- when I try to import a file from EBI-SRA (I paste the ftp address into "Upload File") it's loading without stopping until the drive is full (>97 GB), although the file itself is only about 3GB. Is it a problem with the EBI server or within galaxy?

Thanks for any help.

On Oct 14, 2013, at 5:50 PM, Vipin TS wrote:

Hi Stanislas,

Please check the PATH variable and make sure that you can access bowtie2 from command line and then restart the Galaxy service through cloudman interface. I think that should work.

Vipin

I'm trying to run Galaxy on an Amazon AWS cloud using the normal Cloudman distribution (ami-118bfc78). The instatiated Galaxy however does not contain Bowtie2 and Tophat2, even after updating through the Cloudman Admin section. Although the wrappers are there in the tools directory, when I access it through ssh. I've also installed Bowtie2 manually on the server and the command bowtie2 does get recognized. How cat I get these two to run on the Galaxy instance?

Thanks for your help. Best Stanislas ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

Thanks. I tried both File1 and 2 of SRR618542. Here's one of the links: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR618/SRR618542/SRR618542_1.fastq.gz

On Oct 14, 2013, at 8:01 PM, Vipin TS wrote:

• bowtie2 does not show any built-in reference genomes

by default Cloudman didn't ship the genome index for bowtie2. Bowtie2 use its own index set. Usage: bowtie2-build [option] genome.fa index_basename

and add the entries in "bowtie2_indices.loc". Please make sure that the fields are tab delimited, not space delimited, and have no trailing or extra whitespace (this is easy to slip in by accident). and place the *.loc file under /mnt/galaxyIndices/galaxy/tool-data/

Most of the genome reference file are located at base folder: /mnt/galaxyIndices/genomes/

example: /mnt/galaxyIndices/genomes/Athaliana/araTha_tair9/seq/Arabidopsis_thaliana.TAIR9.55.dna.toplevel.fa.gz

• when I try to import a file from EBI-SRA (I paste the ftp address into "Upload File") it's loading without stopping until the drive is full (>97 GB), although the file itself is only about 3GB. Is it a problem with the EBI server or within galaxy?

I am not sure, can you please paste the url which points to the file.

Thanks for any help.

On Oct 14, 2013, at 5:50 PM, Vipin TS wrote:

...

Hi Stanislas,

Please check the PATH variable and make sure that you can access bowtie2 from command line and then restart the Galaxy service through cloudman interface. I think that should work.

Vipin

I'm trying to run Galaxy on an Amazon AWS cloud using the normal Cloudman distribution (ami-118bfc78). The instatiated Galaxy however does not contain Bowtie2 and Tophat2, even after updating through the Cloudman Admin section. Although the wrappers are there in the tools directory, when I access it through ssh. I've also installed Bowtie2 manually on the server and the command bowtie2 does get recognized. How cat I get these two to run on the Galaxy instance?

Thanks for your help. Best Stanislas ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/