[galaxy-user] Toolshed initial upload errors out
As per the title, I'm trying to setup a toolshed for our local use. After creating a repo, I try to upload the initial file only to get: TypeError: array item must be char Which seems to happen repeatedly, i.e. it's not a passing error. While I'm here, a perhaps obvious question: where or how does the main Galaxy instance get the list of toolsheds to display? The main and test sheds are hardcoded in, I guess, but how does it pick up the local - simply by virtue of the fact that it is local? p Paul Agapow (paul-michael.aga...@hpa.org.uk) Bioinformatics, Health Protection Agency - ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Megablast question
Hi, I am using megablast and was wondering how can I get chromosome number and coordinates of its hits. Thanks Shamesher ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] (no subject)
Hi, I have hit a brick wall when trying to convert wig files from the GEO to bigwig files. Each time I try (and I have tried many times since October), I get the same error. For example, here is a downloaded wig file, that I assigned to the mouse mm8 genome, and the error I got when I tried to convert it to a bigwig file. The dataset came from Bing Ren's lab, and its GEO record is here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM560344 The wig file was uploaded to Galaxy Dec. 8, 2011, and I assigned mm8 rather than mm9 based on the GEO record: 49: GSM560344_03112009_313D2AAXX_B7.wi ~960,000 lines format: wig, database: mm8 Info: uploaded wig file display at UCSC main The details for this upload are as follows: Tool: Upload File Name: GSM560344_03112009_313D2AAXX_B7.wi Created:Dec 08, 2011 Filesize: 12.1 Mb Dbkey: mm8 Format: wig Tool Version: Tool Standard Output: stdout Tool Standard Error:stderr Input Parameter Value File Format auto Genome Conditional (files_metadata)32 Inheritance Chain GSM560344_03112009_313D2AAXX_B7.wi The wig-to-bigWig conversion on data 49 (using the wig to bigwig conversion tool in the convert formats toolbox) was run on March 21, 2012 and gave the following error: 77: Wig-to-bigWig on data 49 0 bytes An error occurred running this job:line 152351 of stdin: chromosome chr13 has 120614378 bases, but item ends at 120614600 line 298005 of stdin: chromosome chr17 has 95177420 bases, but item ends at 95177625 line 325066 of stdin: chromosome chr16 has 98252459 bases, but item ends at 9825252 The details for this operation are as follows: Tool: Wig-to-bigWig Name: Wig-to-bigWig on data 49 Created:Mar 21, 2012 Filesize: 0 bytes Dbkey: mm8 Format: bigwig Tool Version: Tool Standard Output: stdout Tool Standard Error:stderr Input Parameter Value Convert 49: GSM560344_03112009_313D2AAXX_B7.wi Conditional (settings) 1 Items to bundle in r-tree 256 Data points bundled at lowest level 1024 Clip chromosome positions True Do not use compression True Inheritance Chain Wig-to-bigWig on data 49 I gather that the chromosome ends are not being snipped off, even though I toggle this option on the galaxy conversion tool. And I know it's doing something, because if I toggle that option off, I get an error that includes broken pipe and simply aborts. I apologize for knowing so little about the bioinformatics involved here. And I'm sure I've overlooked something that is likely obvious to others and/or failed to provide some critical bit of info in this email. But any help would be greatly appreciated. Thanks, Mike ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] equicktandem search not yielding any results
Hello all, I am certainly new to using galaxy and I have already checked the message boards to get some assistance on this but was unsuccessful. Anyways, here is my problem, I have a a FASTA file of C. gigas partial sequences. I was trying to use Galaxy's equicktandem tool to identify micro satellites in the sequence. However, when I ran the tool it did not yield any results. This is strange because I could visually pick out where l thought the algorithm should have found a hit. Additionally, trimming my collection of sequences to a single sequence did not yield any hits. Moreover, I created a fake sequence with very obvious microsatellites and the algorithm appeared to work fine as it identified the repeats. While I suppose it is certainly possible that there may just not be any microsatellites in my sequence, I find it highly unlikely and suspect something else is going on. This seemed like such a simple tool yet I am having much difficulty in using it. I am simply uploading my FASTA file normally and then taking that file and using the tool. I am doing this all online through the galaxy website not a local instance and if you would like to see yourself the FASTA file can be downloaded at http://genefish.wikispaces.com/crassostreome and the FASTA file is cgigas_alpha_v0.3.2 (the collection of 272 sequences). Please help this has been excruciatingly frustrating for me and I suspect that a veteran Galaxy user may be able to see my error quickly. Best, Harry hpodsch...@gmail.com ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
