Re: [galaxy-dev] read_bits64 error when loading large genomes/data into trackster

. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Mar 25, 2014, at 11:15 AM, Raj Ayyampalayam ra...@uga.edu mailto:ra...@uga.edu wrote: Jeremy, I uploaded my dataset to the main galaxy site and the visualization failed. Here is the link to the history

Re: [galaxy-dev] read_bits64 error when loading large genomes/data into trackster

problem on both main and my local galaxy instances (local is tracking latest galaxy-dist). Thanks, -Raj On Wednesday, March 05, 2014 11:25:26 AM, Raj Ayyampalayam wrote: I checked the version of bx-python egg and confirmed that it is bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs2.egg. I

Re: [galaxy-dev] new data manager can't build bowtie or sam fasta, interface differences, how to fetch ncbi stuff

You are probably missing the samtools and bowtie2 dependencies. Make sure Galaxy can find the binaries. -Raj On Fri Mar 7 00:16:07 2014, Langhorst, Brad wrote: I’m slowly wrapping my head around the new data manager stuff… but I don’t think I quite have it yet. I was able to download hg19

[galaxy-dev] read_bits64 error when loading large genomes/data into trackster

Hello, I am trying to visualize a large genome (Large number of scaffolds) and a large (bam file) in trackster on our local galaxy instance (running release_2014.02.10). When ever I try to do the above I see the following error in the logs: File bbi_file.pyx, line 215, in

Re: [galaxy-dev] Sudden error in local galaxy installation

483, in convert_dataset -Raj On Fri Aug 2 00:51:39 2013, Raj Ayyampalayam wrote: Here is the first part of the error (Traceback): galaxy.tools ERROR 2013-08-01 22:56:16,590 Exception caught while attempting tool execution: Traceback (most recent call last): File /panfs/pstor.storage/home

[galaxy-dev] Sudden error in local galaxy installation

Hello, My local cluster based galaxy installation was running fine till this evening. Later I decided to test some workflows and got an error with massive stack trace. I can't make any sense of this. Here is the last part of the error. The stack trace is literally 1000's of lines. Can

Re: [galaxy-dev] Sudden error in local galaxy installation

= build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name Thanks, -Raj On 8/2/13 12:00 AM, Raj Ayyampalayam wrote: Hello, My local cluster based galaxy installation was running fine till this evening. Later I decided to test some workflows and got an error with massive stack trace. I can't make any sense of this. Here

[galaxy-dev] Storage question for Galaxy-Admins

Hello, I am trying to come up with a number for our local galaxy storage requirements when we go live (This is an installation for research at our university). I checked out the survey that was done a while back for the GalaxyAdmins. It seems that the bigger installations have allocated

Re: [galaxy-dev] Trinity wrapper not working on local installation

is library_type is None and library_type is not None. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Thu, Mar 28, 2013 at 6:35 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Mar 28, 2013 at 4:36 AM, Raj Ayyampalayam ra...@uga.edu wrote: Hello, I am trying to get

[galaxy-dev] Trinity wrapper not working on local installation

Hello, I am trying to get the trinity wrapper to work on our local galaxy installation using the latest trinity version. The main issue is that the Trinity.pl call has --SS_lib_type None in the script file. The data I am using is unstranded paired end reads and I am selecting None in the

[galaxy-dev] Uploading large data sets from cluster file system for local galaxy install

Hello, I have a question for the many galaxy admins here. I am in the process of setting up a local galaxy install submitting the jobs as real users to our local SGE cluster. I am trying to figure out the best way to load large datasets (Sequence files etc..) stored in the local clusters

Re: [galaxy-dev] Problem running ncbi_makeblastdb as real user in cluster

Hi Guys, Thanks for the quick response. I installed the latest blast datatypes from the toolshed and that fixed the issue. Peter, can you also fix the $outfile.extra_files_path to $outfile.files_path on line 5 in the makedb wrapper xml file. Thanks, -Raj On Wednesday, March 20, 2013

Re: [galaxy-dev] Problems with rsync from datacache.g2.bx.psu.edu/indexes

Hi Nate, I am trying to rsync the indexes and getting a rsync error. $ rsync -avz rsync://datacache.g2.bx.psu.edu/indexes/phiX . @ERROR: chroot failed rsync error: error starting client-server protocol (code 5) at main.c(1530) [receiver=3.0.6] Should I change anything in my command? Thanks,

[galaxy-dev] Problem running ncbi_makeblastdb as real user in cluster

Hello, I am setting up a local galaxy installation and using our local SGE cluster to run the jobs as real users. One of the first few tools I tested was the ncbi makebkastdb tool. When I try to run it the history for that particular job is immediately shown as follows: 0: (unnamed

Re: [galaxy-dev] How to upload local files in Galaxy

Hello, I am interested in this local upload file tool. Can you please send the files to me as well. Thanks. -Raj On 6/8/12 4:36 AM, Alban Lermine wrote: Hi, There is also another solution if you don't want let users being able to create libraries. We have implemented this solution in our