Re: [galaxy-user] Quality trimming of sequences before RNA-Seq
Dear Noa, I also feel the same. So I think it would be better to use these three steps remove sequencing artifacts then trim the sequences by from the 5' end or if needed from the 3'end also (2-5 bases, depending on your sequence quality) finally filter the sequences by quality (I used the default parameters). Although it removed 15% of the sequences but I feel confident with the high quality data. Any better suggestion will be appreciated. CHeers, Bomba On Thu, Mar 1, 2012 at 10:48 AM, Noa Sher noa.s...@gmail.com wrote: Hi I am looking at various options of quality trimming sequences for RNA Seq analysis I know I can chop off a certain number of bases off the 3' or 5' ends of the reads. Is it possible to use a sliding window to chop reads to different lengths, leaving everything above quality score 20 (for example) or would this be inadvisable as the differing lengths of reads would skew the downstream FPKM analysis? Thanks noa ___ 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/ -- Dr. BOMBA DAM Alexander von Humboldt Postdoctoral Research Fellow Max-Planck-Institut für terrestrische Mikrobiologie Karl-von-Frisch-Straße 10 D-35043 Marburg, Germany E mail: bomba@mpi-marburg.mpg.de PHONE: +49 176 321 321 75 (Mobile); +49 6421 178 721 (LAB); +49 6421 2828516 (ROOM) Assistant Professor of Microbiology Department of Botany, Institute of Science Visva-Bharati (A Central University) Santiniketan, West Bengal 731235, India. E mail: bumba_mi...@visva-bhatari.ac.in, bumba_mi...@rediffmail.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/
Re: [galaxy-user] Filtering reads on wrong strand before FPKM scoring on cufflinks
Dear Noa, Bowtie in --besthttp://bowtie-bio.sourceforge.net/manual.shtml#bowtie-options-bestmode eliminates strand bias by forcing Bowtie to select one strand or the other with a probability that is proportional to the number of best sites on the strand. try with this mode. I am also trying to do the same. If you find any good alternative for the whole process please let me know. Bomba On Thu, Mar 1, 2012 at 11:22 AM, Noa Sher noa.s...@gmail.com wrote: Hi I am running sequencing data from a directional RNASeq protocol on bowtie (it is a bacterial genome) and then cuffdiff or cufflinks. I occasionally see a few reads that align to the wrong direction (opposite strand). Is there any way to filter these out before I do my FPKM analysis? Thanks Noa ___ 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/ -- Dr. BOMBA DAM Alexander von Humboldt Postdoctoral Research Fellow Max-Planck-Institut für terrestrische Mikrobiologie Karl-von-Frisch-Straße 10 D-35043 Marburg, Germany E mail: bomba@mpi-marburg.mpg.de PHONE: +49 176 321 321 75 (Mobile); +49 6421 178 721 (LAB); +49 6421 2828516 (ROOM) Assistant Professor of Microbiology Department of Botany, Institute of Science Visva-Bharati (A Central University) Santiniketan, West Bengal 731235, India. E mail: bumba_mi...@visva-bhatari.ac.in, bumba_mi...@rediffmail.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/
[galaxy-user] Metagenomics
Hello I am a relatively new user on Galaxy and I had a question regarding Fetching Taxonomic Information. It is great that I can retrieve all of the hits for each sequence, but I cannot seem to find an option to also provide how accurate of a match it is to the given taxon. For instance, a percentage match. I can access this information in the original file and programmatically retrieve it but, it would be nice if it came in one package so that I can avoide those false hits that have a low percentage match. Can you please provide me with instructions on how to best to retrieve this information (hopefully in a single file)? Thank you Vincent ___ 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] Getting errors trying to enable samtools_mpileup
I am running a local copy of Galaxy, last ran 'hg pull -u' on 2/20/12. I am trying to enable use of Mpileup for SAM Tools, and have added the entry for the samtools_mpileup.xml file in tool_conf.xml. However, when I startup Galaxy, the link for Mpileup does not appear in the Tools pane, and I see the following errors from the Galaxy startup: galaxy.tools ERROR 2012-02-29 16:28:51,919 error reading tool from path: samtools/samtools_mpileup.xml Traceback (most recent call last): File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py, line 212, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py, line 305, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py, line 531, in __init__ self.parse( root, guid=guid ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py, line 641, in parse self.parse_inputs( root ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py, line 723, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py, line 922, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py, line 989, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py, line 945, in parse_input_elem group.inputs = self.parse_input_elem( elem, enctypes, context ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py, line 1015, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py, line 1027, in parse_param_elem param = ToolParameter.build( self, input_elem ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py, line 176, in build return parameter_types[param_type]( tool, param ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py, line 1330, in __init__ ToolParameter.__init__( self, tool, elem ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py, line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/validation.py, line 23, in from_element return validator_types[type].from_element( param, elem ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/validation.py, line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/data/__init__.py, line 21, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'sam_fa_indexes' Can someone tell me what is wrong here? Am I missing something in the database? Thanks, Mike Waldron ___ 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] Getting errors trying to enable samtools_mpileup
Hello Mike, I am going to move your question over to the galaxy-...@bx.psu.edu mailing list, which is for the discussion of local instance questions. Some things to double check: SAMTools is already set up correctly, with indexes? http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup - see SAM Tools installation If you are still running pile-up, note that two versions of SAMTools are required: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies Including some reorganization to accommodate both versions, as explained in this wiki: http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies Hopefully this helps, Best, Jen Galaxy team On 3/1/12 5:49 AM, Waldron, Michael H wrote: I am running a local copy of Galaxy, last ran 'hg pull -u' on 2/20/12. I am trying to enable use of Mpileup for SAM Tools, and have added the entry for the samtools_mpileup.xml file in tool_conf.xml. However, when I startup Galaxy, the link for Mpileup does not appear in the Tools pane, and I see the following errors from the Galaxy startup: galaxy.tools ERROR 2012-02-29 16:28:51,919 error reading tool from path: samtools/samtools_mpileup.xml Traceback (most recent call last): File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py, line 212, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py, line 305, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py, line 531, in __init__ self.parse( root, guid=guid ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py, line 641, in parse self.parse_inputs( root ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py, line 723, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py, line 922, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py, line 989, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py, line 945, in parse_input_elem group.inputs = self.parse_input_elem( elem, enctypes, context ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py, line 1015, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py, line 1027, in parse_param_elem param = ToolParameter.build( self, input_elem ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py, line 176, in build return parameter_types[param_type]( tool, param ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py, line 1330, in __init__ ToolParameter.__init__( self, tool, elem ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py, line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/validation.py, line 23, in from_element return validator_types[type].from_element( param, elem ) File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/validation.py, line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File /nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/data/__init__.py, line 21, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'sam_fa_indexes' Can someone tell me what is wrong here? Am I missing something in the database? Thanks, Mike Waldron ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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/
Re: [galaxy-user] Metagenomics
Vincent Great question!!! And a follow up for me, is how to purge the conserved sequences. Presently the current data set I have from Fetch is likely to be 99% composed of incorrect taxon just because of conserved sequence. So, how do you select just unique sequences (ie those that do not have more then... say 5 hits above 99%). Any advice would be nice. Our bioinformatic person said there was a way to do it thru blast X. Scott Scott Tighe Advanced Genome Technology Lab Vermont Cancer Center at the University of Vermont 149 Beaumont Avenue Health Science Research Bd RM 305 Burlington Vermont USA 05405 lab 802-656-AGTC (2482) cell 802-999- On 2/29/2012 8:32 PM, Montoya, Vincent wrote: Hello I am a relatively new user on Galaxy and I had a question regarding Fetching Taxonomic Information. It is great that I can retrieve all of the hits for each sequence, but I cannot seem to find an option to also provide how accurate of a match it is to the given taxon. For instance, a percentage match. I can access this information in the original file and programmatically retrieve it but, it would be nice if it came in one package so that I can avoide those false hits that have a low percentage match. Can you please provide me with instructions on how to best to retrieve this information (hopefully in a single file)? Thank you Vincent ___ 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/ ___ 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/
Re: [galaxy-user] [galaxy-bugs] GI errors in the megablast table of results ?
Hello all, Did this issue get resolved? If Sandrine was right about there being an off by one error in GI number in the BLAST tabular output, it could be a bug in 'legacy' blastall command. I say 'legacy' BLAST because that's what Galay's NGS 'megablast' tool is using internally (as opposed to the the NCBI's replacement BLAST+). Peter On Wed, Jan 25, 2012 at 3:14 PM, Guru Ananda g...@psu.edu wrote: Dear Sandrine, Thanks for pointing out this issue. The BLAST databases we have on Galaxy are from last year, while those on NCBI website are the latest (Jan 2012). As pointed out on NCBI website (http://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html), it appears that each time any change is made to a sequence/database, GI numbers change as well. This is perhaps why you're observing discrepancies in GI numbers and lengths between megablast outputs on Galaxy and NCBI. I'm currently in the process of downloading the latest BLAST databases from NCBI, and I'll let you know when they're available for use on Galaxy. Thanks for your patience, Guru Galaxy team. On Wed, Nov 9, 2011 at 8:03 AM, Sandrine Hughes sandrine.hug...@ens-lyon.fr wrote: Dear all, I’m not sure where I need to send my email so I apologize if I’m wrong. I have a trouble with the Megablast program available in NGS Mapping and I hope that you can help. Indeed, I think that there might be a problem with the table given in output, and notably a shift between the GI numbers and the parameters associated. Here are the details: I. First, what I have done : I used the program to identify the species that I have in a mix of sequences by using the following options: Database nt 27-Jun-2011 Word size 16 Identity 90.0 Cutoff 0.001 Filter out low complexity regions Yes I run the analyses twice and obtained exactly the same results (I used the online version of Galaxy, not a local one). II. Second, I analysed the data obtained for one of my sequence (1-202). The following lines are the beginning of the table that I obtained after the megablast and two lines with troubles: 1-202 312182292 484 99.33 150 1 0 1 150 1 150 2e-75 289.0 1-202 312182201 476 99.33 150 1 0 1 150 1 150 2e-75 289.0 1-202 308228725 928 99.33 150 1 0 1 150 19 168 2e-75 289.0 1-202 308228711 938 99.33 150 1 0 1 150 22 171 2e-75 289.0 1-202 308197083 459 99.33 150 1 0 1 150 10 159 2e-75 289.0 1-202 300392378 920 99.33 150 1 0 1 150 10 159 2e-75 289.0 1-202 300392376 918 99.33 150 1 0 1 150 9 158 2e-75 289.0 1-202 300392375 922 99.33 150 1 0 1 150 11 160 2e-75 289.0 1-202 300392374 931 99.33 150 1 0 1 150 21 170 2e-75 289.0 1-202 300392373 909 99.33 150 1 0 1 150 21 170 2e-75 289.0 1-202 300392371 1172 99.33 150 1 0 1 150 9 158 2e-75 289.0 ... 1-202 179366399 151762 98.67 150 2 0 1 150 46880 47029 6e-73 281.0 1-202 58617849 511 98.67 150 2 0 1 150 21 170 6e-73 281.0 III. Third, what I’ve noticed: My first trouble was that among all the species identified, two were very different from the expected ones (2 last lines). So I decided to search if that could be possible for that sequence and performed independently a megablast on the NCBI with similar options. I was not able to find these two species in the results. So, I decided to check the hits identified in the table above and identified a second trouble. In the table, the second column give the GI of the database hit and the third column give the length of the database hit. However, when I manually checked in NCBI the length of the GI, this one was incorrect. Indeed, for the GI 312182292, the length should be 580 and not 484. By checking different lines, I noticed that the length that is given for a GI corresponds to the length of the GI-1. As you can see in the above table, some GI are consecutive (300392376, 300392375,...). When checking the length of 300392376 in NCBI, I should have 920. But when I checked 300392375, I found 918. And this was true for the following lines : 300392374 give normally 922 and 300392373 give 931... My conclusion at that point was that there was a shift of –1 between the GI and the other parameters of the line (indeed the parameters for the remaining columns are in agreement with the
Re: [galaxy-user] Error in DepthOfCoverage (GATK) tool
Hi Raj, Thanks for reporting, this issue has been resolved in changeset 6778:35be930b21be. Please let us know if you encounter further issues. Thanks for using Galaxy, Dan On Mar 1, 2012, at 3:30 AM, Praveen Raj Somarajan wrote: Hello, I'm facing an issue with Depth Of Coverage tool when it runs on refGene and target BED file. The error message is: File cheetah_DynamicallyCompiledCheetahTemplate_1330588825_26_16118.py, line 402, in respond NotFound: cannot find 'omit_interval_statistics' while searching for 'gatk_param_type.omit_interval_statistics' I noticed that the issue is only when the Advanced GATK options is enabled to set target BED file. The commandline runs perfectly with the input files, but galaxy fails due to this error. Can anyone suggest what's the issue? Best, Raj This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD ___ 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/ ___ 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] PE reads d ont map after trimming
Hi, I hoped that someone could shed some light onto this . I am attempting to map a set of 2x 150 illumina PE data from a DNA resequencing project. The run had an issue where the quality of the last 50 or so reads of the second run tail off quite considerably. I thought to trim the second read such that the poorer sequence bases are stripped form the end of the read. I attempted to do this using the FASTQ quality trimmer then mapping both reads using bowtie. When I did this however, I went from an alignment of 34% passing filter reads aligned not trimmed (which is not good to start off with), to 0.18%. trim command was set as defaults: Any ideas what I could be doing wrong? This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere For more information and to find out how you can switch, visit www.connectingforhealth.nhs.uk/nhsmail ___ 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/
Re: [galaxy-user] Speed up uploading into local Galaxy, terribly slow!!
Thanks Jennifer, I already uncomment and add my email address but still the admin link does not appear. I then registered my email in users and logged in with that email address and I still don't see the link. when I type /admin at the of the url it says that I have to be logged in as an administrator. sorry I am a newbe on this admin stuff. From: Jennifer Jackson j...@bx.psu.edu To: Alejandra Rougon alerou...@yahoo.com Cc: galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu; closetic...@galaxyproject.org closetic...@galaxyproject.org Sent: Tuesday, 28 February 2012, 17:19 Subject: Re: [galaxy-user] Speed up uploading into local Galaxy, terribly slow!! Hi, You will want to assign yourself as an administrator in the universe_wsgi.ini file. # Administrative users - set this to a comma-separated list of valid Galaxy # users (email addresses). These users will have access to the Admin section # of the server, and will have access to create users, groups, roles, # libraries, and more. For more information, see: # http://wiki.g2.bx.psu.edu/Admin/Interface #admin_users = None ^^ uncomment and add your login email here Other wikis that may be helpful, especially if user login is not yet set up: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server http://wiki.g2.bx.psu.edu/Admin/Config Hopefully this helps, Jen Galaxy team On 2/28/12 2:59 PM, Alejandra Rougon wrote: Thank you Greg, I saw the wiki but I do not see the admin link in my galaxy interface. How do you open galaxy as an administrator? t *From:* Greg Von Kuster g...@bx.psu.edu *To:* Alejandra Rougon alerou...@yahoo.com *Cc:* galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu *Sent:* Tuesday, 28 February 2012, 14:02 *Subject:* Re: [galaxy-user] Speed up uploading into local Galaxy, terribly slow!! You can upload your large file to Galaxy data libraries using a combination of Upload files from filesystem paths and Do not copy data into Galaxy's default file store. See this wiki: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files For all of the information on Galaxy data libraries, see this wiki: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries Greg Von Kuster On Feb 28, 2012, at 2:54 PM, Alejandra Rougon wrote: Hello, I tried to search in the forums and although this question has appeared many times I still don't have a solution. I cannot manage to upload big files into the local galaxy, it just takes ages. Can I not just copy and paste into a local directory? why do I have to upload the files if it is already installed locally? I do not have a server webpage in order to use the url address option If I do it through ftp (locally) what ftp address shall I put? ftp localhost:8080?? Is there any other option to speed up uploading, is so slow that is no longer worth using it, please help me! ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org http://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/ ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support___ 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/
Re: [galaxy-user] Speed up uploading into local Galaxy, terribly slow!!
Do you restart your Galaxy server when you make changes to universe_wsgi.ini (like adding / uncommenting email addresses for the admin_users setting)? On Mar 1, 2012, at 12:56 PM, Alejandra Rougon wrote: Thanks Jennifer, I already uncomment and add my email address but still the admin link does not appear. I then registered my email in users and logged in with that email address and I still don't see the link. when I type /admin at the of the url it says that I have to be logged in as an administrator. sorry I am a newbe on this admin stuff. From: Jennifer Jackson j...@bx.psu.edu To: Alejandra Rougon alerou...@yahoo.com Cc: galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu; closetic...@galaxyproject.org closetic...@galaxyproject.org Sent: Tuesday, 28 February 2012, 17:19 Subject: Re: [galaxy-user] Speed up uploading into local Galaxy, terribly slow!! Hi, You will want to assign yourself as an administrator in the universe_wsgi.ini file. # Administrative users - set this to a comma-separated list of valid Galaxy # users (email addresses). These users will have access to the Admin section # of the server, and will have access to create users, groups, roles, # libraries, and more. For more information, see: # http://wiki.g2.bx.psu.edu/Admin/Interface #admin_users = None ^^ uncomment and add your login email here Other wikis that may be helpful, especially if user login is not yet set up: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server http://wiki.g2.bx.psu.edu/Admin/Config Hopefully this helps, Jen Galaxy team On 2/28/12 2:59 PM, Alejandra Rougon wrote: Thank you Greg, I saw the wiki but I do not see the admin link in my galaxy interface. How do you open galaxy as an administrator? t *From:* Greg Von Kuster g...@bx.psu.edu *To:* Alejandra Rougon alerou...@yahoo.com *Cc:* galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu *Sent:* Tuesday, 28 February 2012, 14:02 *Subject:* Re: [galaxy-user] Speed up uploading into local Galaxy, terribly slow!! You can upload your large file to Galaxy data libraries using a combination of Upload files from filesystem paths and Do not copy data into Galaxy's default file store. See this wiki: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files For all of the information on Galaxy data libraries, see this wiki: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries Greg Von Kuster On Feb 28, 2012, at 2:54 PM, Alejandra Rougon wrote: Hello, I tried to search in the forums and although this question has appeared many times I still don't have a solution. I cannot manage to upload big files into the local galaxy, it just takes ages. Can I not just copy and paste into a local directory? why do I have to upload the files if it is already installed locally? I do not have a server webpage in order to use the url address option If I do it through ftp (locally) what ftp address shall I put? ftp localhost:8080?? Is there any other option to speed up uploading, is so slow that is no longer worth using it, please help me! ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org http://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/ ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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
Re: [galaxy-user] Speed up uploading into local Galaxy, terribly slow!!
I did close the web browser and opened it again was that enough? From: Greg Von Kuster g...@bx.psu.edu To: Alejandra Rougon alerou...@yahoo.com Cc: Jennifer Jackson j...@bx.psu.edu; galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu; closetic...@galaxyproject.org closetic...@galaxyproject.org Sent: Thursday, 1 March 2012, 12:46 Subject: Re: [galaxy-user] Speed up uploading into local Galaxy, terribly slow!! Do you restart your Galaxy server when you make changes to universe_wsgi.ini (like adding / uncommenting email addresses for the admin_users setting)? On Mar 1, 2012, at 12:56 PM, Alejandra Rougon wrote: Thanks Jennifer, I already uncomment and add my email address but still the admin link does not appear. I then registered my email in users and logged in with that email address and I still don't see the link. when I type /admin at the of the url it says that I have to be logged in as an administrator. sorry I am a newbe on this admin stuff. From: Jennifer Jackson j...@bx.psu.edu To: Alejandra Rougon alerou...@yahoo.com Cc: galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu; closetic...@galaxyproject.org closetic...@galaxyproject.org Sent: Tuesday, 28 February 2012, 17:19 Subject: Re: [galaxy-user] Speed up uploading into local Galaxy, terribly slow!! Hi, You will want to assign yourself as an administrator in the universe_wsgi.ini file. # Administrative users - set this to a comma-separated list of valid Galaxy # users (email addresses). These users will have access to the Admin section # of the server, and will have access to create users, groups, roles, # libraries, and more. For more information, see: # http://wiki.g2.bx.psu.edu/Admin/Interface #admin_users = None ^^ uncomment and add your login email here Other wikis that may be helpful, especially if user login is not yet set up: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server http://wiki.g2.bx.psu.edu/Admin/Config Hopefully this helps, Jen Galaxy team On 2/28/12 2:59 PM, Alejandra Rougon wrote: Thank you Greg, I saw the wiki but I do not see the admin link in my galaxy interface. How do you open galaxy as an administrator? t *From:* Greg Von Kuster g...@bx.psu.edu *To:* Alejandra Rougon alerou...@yahoo.com *Cc:* galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu *Sent:* Tuesday, 28 February 2012, 14:02 *Subject:* Re: [galaxy-user] Speed up uploading into local Galaxy, terribly slow!! You can upload your large file to Galaxy data libraries using a combination of Upload files from filesystem paths and Do not copy data into Galaxy's default file store. See this wiki: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files For all of the information on Galaxy data libraries, see this wiki: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries Greg Von Kuster On Feb 28, 2012, at 2:54 PM, Alejandra Rougon wrote: Hello, I tried to search in the forums and although this question has appeared many times I still don't have a solution. I cannot manage to upload big files into the local galaxy, it just takes ages. Can I not just copy and paste into a local directory? why do I have to upload the files if it is already installed locally? I do not have a server webpage in order to use the url address option If I do it through ftp (locally) what ftp address shall I put? ftp localhost:8080?? Is there any other option to speed up uploading, is so slow that is no longer worth using it, please help me! ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org http://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/ ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ The Galaxy User
Re: [galaxy-user] Speed up uploading into local Galaxy, terribly slow!!
No, you'll need to stop and restart your Galaxy server. On Mar 1, 2012, at 2:01 PM, Alejandra Rougon wrote: I did close the web browser and opened it again was that enough? From: Greg Von Kuster g...@bx.psu.edu To: Alejandra Rougon alerou...@yahoo.com Cc: Jennifer Jackson j...@bx.psu.edu; galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu; closetic...@galaxyproject.org closetic...@galaxyproject.org Sent: Thursday, 1 March 2012, 12:46 Subject: Re: [galaxy-user] Speed up uploading into local Galaxy, terribly slow!! Do you restart your Galaxy server when you make changes to universe_wsgi.ini (like adding / uncommenting email addresses for the admin_users setting)? On Mar 1, 2012, at 12:56 PM, Alejandra Rougon wrote: Thanks Jennifer, I already uncomment and add my email address but still the admin link does not appear. I then registered my email in users and logged in with that email address and I still don't see the link. when I type /admin at the of the url it says that I have to be logged in as an administrator. sorry I am a newbe on this admin stuff. From: Jennifer Jackson j...@bx.psu.edu To: Alejandra Rougon alerou...@yahoo.com Cc: galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu; closetic...@galaxyproject.org closetic...@galaxyproject.org Sent: Tuesday, 28 February 2012, 17:19 Subject: Re: [galaxy-user] Speed up uploading into local Galaxy, terribly slow!! Hi, You will want to assign yourself as an administrator in the universe_wsgi.ini file. # Administrative users - set this to a comma-separated list of valid Galaxy # users (email addresses). These users will have access to the Admin section # of the server, and will have access to create users, groups, roles, # libraries, and more. For more information, see: # http://wiki.g2.bx.psu.edu/Admin/Interface #admin_users = None ^^ uncomment and add your login email here Other wikis that may be helpful, especially if user login is not yet set up: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server http://wiki.g2.bx.psu.edu/Admin/Config Hopefully this helps, Jen Galaxy team On 2/28/12 2:59 PM, Alejandra Rougon wrote: Thank you Greg, I saw the wiki but I do not see the admin link in my galaxy interface. How do you open galaxy as an administrator? t *From:* Greg Von Kuster g...@bx.psu.edu *To:* Alejandra Rougon alerou...@yahoo.com *Cc:* galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu *Sent:* Tuesday, 28 February 2012, 14:02 *Subject:* Re: [galaxy-user] Speed up uploading into local Galaxy, terribly slow!! You can upload your large file to Galaxy data libraries using a combination of Upload files from filesystem paths and Do not copy data into Galaxy's default file store. See this wiki: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files For all of the information on Galaxy data libraries, see this wiki: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries Greg Von Kuster On Feb 28, 2012, at 2:54 PM, Alejandra Rougon wrote: Hello, I tried to search in the forums and although this question has appeared many times I still don't have a solution. I cannot manage to upload big files into the local galaxy, it just takes ages. Can I not just copy and paste into a local directory? why do I have to upload the files if it is already installed locally? I do not have a server webpage in order to use the url address option If I do it through ftp (locally) what ftp address shall I put? ftp localhost:8080?? Is there any other option to speed up uploading, is so slow that is no longer worth using it, please help me! ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org http://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/ ___ 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:
Re: [galaxy-user] Error in DepthOfCoverage (GATK) tool
Hello Dan, But, I am currently using the latest update of Galaxy (as 'hg incoming' says 'no changes'). Just to clarify one thing: which repository should I clone - https://bitbucket.org/galaxy/galaxy-dist/ (mentioned in GetGalaxy.org) OR http://www.bx.psu.edu/hg/galaxy/ (mentioned in NewsBrief website). I use the first one to update Galaxy. I tried to pull the below changeset, but it says 'invalid revision'. Please suggest. Best, Raj From: Daniel Blankenberg [mailto:d...@bx.psu.edu] Sent: Thursday, March 01, 2012 8:45 PM To: Praveen Raj Somarajan Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Error in DepthOfCoverage (GATK) tool Hi Raj, Thanks for reporting, this issue has been resolved in changeset 6778:35be930b21be. Please let us know if you encounter further issues. Thanks for using Galaxy, Dan On Mar 1, 2012, at 3:30 AM, Praveen Raj Somarajan wrote: Hello, I'm facing an issue with Depth Of Coverage tool when it runs on refGene and target BED file. The error message is: File cheetah_DynamicallyCompiledCheetahTemplate_1330588825_26_16118.py, line 402, in respond NotFound: cannot find 'omit_interval_statistics' while searching for 'gatk_param_type.omit_interval_statistics' I noticed that the issue is only when the Advanced GATK options is enabled to set target BED file. The commandline runs perfectly with the input files, but galaxy fails due to this error. Can anyone suggest what's the issue? Best, Raj This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://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/ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD___ 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/
