Re: [galaxy-dev] DESeq for Galaxy
Hi Ross, I tried installing again it shows no item.. Also i couldn't find any .log file or the ( /htseq/0.5.4p3/fubar/htseq_bams_to_count_matrix) in the tool dependency directory. Thanks On Wed, Aug 21, 2013 at 12:13 PM, Ross wrote: > Sridhar, > Kindly try rerunning the failed job to confirm that it still fails now > that the tool installation should have well and truly finished - it does > take a while. > If it still fails the same way, please send me a copy of the installation > log for the htseq dependency found in: > [your > tool_dependency_directory]/htseq/0.5.4p3/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/INSTALLATION.log > > > > On Wed, Aug 21, 2013 at 4:38 PM, Sridhar Srinivasan < > sridhar2bioi...@gmail.com> wrote: > >> Hi Ross, >> >> >> i Installed through admin interface . >> for pysam and freetype it showed new... and rest installed.. >> >> >> Thanks >> >> >> >> On Wed, Aug 21, 2013 at 11:47 AM, Ross wrote: >> >>> Sridhar, >>> The error message you provide suggests that the HTSeq python module is >>> not available when Galaxy tries to run the tool. >>> Please confirm that you installed that tool through the admin interface >>> from the test toolshed and that the admin interface for toolshed installed >>> tools shows the installed repository in your Galaxy instance has the htseq >>> dependency successfully installed like the end of the page below : >>> >>> >>> >>>- Repository Actions >>> >>> Installed tool shed repository 'htseq_bams_to_count_matrix' >>> Tool shed:testtoolshed.g2.bx.psu.edu >>> Name:htseq_bams_to_count_matrix >>> Description: >>> Revision:f69b55c71ae5 >>> Owner:fubar >>> Location:/mnt/galaxy/shed_tools/ >>> testtoolshed.g2.bx.psu.edu/repos/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/htseq_bams_to_count_matrix >>> Deleted:False >>> >>> Dependencies of this repository >>> >>> Installed repository dependencies >>> NameRevisionOwner Installation >>> statuspackage_numpy_1_7<http://115.146.84.239/admin_toolshed/manage_repository?id=148934b1ed5706b5> >>> af9633757cf0blankenbergInstalledpackage_pysam_0_7_5<http://115.146.84.239/admin_toolshed/manage_repository?id=96c0d701aac155a0> >>> a4e35f23093ffubarInstalledpackage_freetype_2_4<http://115.146.84.239/admin_toolshed/manage_repository?id=dee0124e4d3ab063> >>> 4e54e357ac25bgrueningInstalledpackage_matplotlib_lite<http://115.146.84.239/admin_toolshed/manage_repository?id=c32939704028ccc3> >>> 8df6bbf48c3afubarInstalled >>> >>> Installed tool dependencies* - click the name to browse the dependency >>> installation directory* >>> NameVersionTypeInstallation >>> statusfreetype<http://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52&id=148934b1ed5706b5> >>> 2.4.11packagematplotliblite<http://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52&id=dee0124e4d3ab063> >>> 1.2.1packagenumpy<http://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52&id=94e61e06dbd29e52> >>> 1.7.1packagepysam<http://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52&id=c32939704028ccc3> >>> 0.7.5packagehtseq<http://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52&id=96c0d701aac155a0> >>> 0.5.4p3package >>> >>> >>> >>> >>> On Wed, Aug 21, 2013 at 4:05 PM, Sridhar Srinivasan < >>> sridhar2bioi...@gmail.com> wrote: >>> >>>> Hi All, >>>> >>>> I installed the toolshed htseq_bams_to_count_matrix repository , i >>>> gave the gene model gtf file(ex: tss.gtf file) Gene model (GFF) file >>>> to count reads over from your current history: in this section and all >>>> bam files. >>>> >>>> it gives error as " >>>> empty >>>> format: tabular, database: hg19 >>>> Traceback (most recent call last): File "/data/galaxy/shed_tools/ >>>> testtoolshed.g2.bx.psu.edu/repos/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/htseq_bams_to_count_matrix/htseq_bams_to_count_matrix/htseqsams2mx.py", >>>> line 45, in import HTSeq.scripts.count as htcount " >>>> >>>> Thanks >>>> >>>> >>>> >>>> >>>> On We
Re: [galaxy-dev] DESeq for Galaxy
Hi Ross, i Installed through admin interface . for pysam and freetype it showed new... and rest installed.. Thanks On Wed, Aug 21, 2013 at 11:47 AM, Ross wrote: > Sridhar, > The error message you provide suggests that the HTSeq python module is not > available when Galaxy tries to run the tool. > Please confirm that you installed that tool through the admin interface > from the test toolshed and that the admin interface for toolshed installed > tools shows the installed repository in your Galaxy instance has the htseq > dependency successfully installed like the end of the page below : > > > >- Repository Actions > > Installed tool shed repository 'htseq_bams_to_count_matrix' > Tool shed:testtoolshed.g2.bx.psu.edu > Name:htseq_bams_to_count_matrix > Description: > Revision:f69b55c71ae5 > Owner:fubar > Location:/mnt/galaxy/shed_tools/ > testtoolshed.g2.bx.psu.edu/repos/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/htseq_bams_to_count_matrix > Deleted:False > > Dependencies of this repository > > Installed repository dependencies > NameRevisionOwner Installation > statuspackage_numpy_1_7<http://115.146.84.239/admin_toolshed/manage_repository?id=148934b1ed5706b5> > af9633757cf0blankenbergInstalledpackage_pysam_0_7_5<http://115.146.84.239/admin_toolshed/manage_repository?id=96c0d701aac155a0> > a4e35f23093ffubarInstalledpackage_freetype_2_4<http://115.146.84.239/admin_toolshed/manage_repository?id=dee0124e4d3ab063> > 4e54e357ac25bgrueningInstalledpackage_matplotlib_lite<http://115.146.84.239/admin_toolshed/manage_repository?id=c32939704028ccc3> > 8df6bbf48c3afubarInstalled > > Installed tool dependencies* - click the name to browse the dependency > installation directory* > NameVersionTypeInstallation > statusfreetype<http://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52&id=148934b1ed5706b5> > 2.4.11packagematplotliblite<http://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52&id=dee0124e4d3ab063> > 1.2.1packagenumpy<http://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52&id=94e61e06dbd29e52> > 1.7.1packagepysam<http://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52&id=c32939704028ccc3> > 0.7.5packagehtseq<http://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52&id=96c0d701aac155a0> > 0.5.4p3package > > > > > On Wed, Aug 21, 2013 at 4:05 PM, Sridhar Srinivasan < > sridhar2bioi...@gmail.com> wrote: > >> Hi All, >> >> I installed the toolshed htseq_bams_to_count_matrix repository , i gave >> the gene model gtf file(ex: tss.gtf file) Gene model (GFF) file to count >> reads over from your current history: in this section and all bam files. >> >> it gives error as " >> empty >> format: tabular, database: hg19 >> Traceback (most recent call last): File "/data/galaxy/shed_tools/ >> testtoolshed.g2.bx.psu.edu/repos/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/htseq_bams_to_count_matrix/htseq_bams_to_count_matrix/htseqsams2mx.py", >> line 45, in import HTSeq.scripts.count as htcount " >> >> Thanks >> >> >> >> >> On Wed, Aug 21, 2013 at 10:44 AM, Mahtab Mirmomeni < >> m.mirmom...@student.unimelb.edu.au> wrote: >> >>> You can use htseq_bams_to_count_matrix repository by fubar in the test >>> toolshed. >>> >>> >>> On Wed, Aug 21, 2013 at 2:37 PM, Sridhar Srinivasan < >>> sridhar2bioi...@gmail.com> wrote: >>> >>>> Hi All, >>>> >>>> Thanks for the suggestions. I installed the Toolshed ( >>>> Differential_Count (version 0.21) ). It asks for the input matrix - rows >>>> are contigs, columns are counts for each sample. >>>> Any idea on how to generate this matrix file?? >>>> >>>> Thanks >>>> >>>> >>>> On Tue, Aug 20, 2013 at 12:53 PM, Mahtab Mirmomeni < >>>> m.mirmom...@student.unimelb.edu.au> wrote: >>>> >>>>> Hi Sridhar, >>>>> >>>>> I'm using differential_count_model repository by fubar in the test >>>>> toolshed which has both EdgeR and Deseq2 and it's working for me. >>>>> >>>>> Thanks >>>>> Mahtab >>>>> >>>>> >>>>> On Tue, Aug 20, 2013 at 5:03 PM, Bjoern Gruening < >>>>> bjoern.gruen...@gmail.com> wrote: >>>>> >>>>
Re: [galaxy-dev] DESeq for Galaxy
Hi All, I installed the toolshed htseq_bams_to_count_matrix repository , i gave the gene model gtf file(ex: tss.gtf file) Gene model (GFF) file to count reads over from your current history: in this section and all bam files. it gives error as " empty format: tabular, database: hg19 Traceback (most recent call last): File "/data/galaxy/shed_tools/ testtoolshed.g2.bx.psu.edu/repos/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/htseq_bams_to_count_matrix/htseq_bams_to_count_matrix/htseqsams2mx.py", line 45, in import HTSeq.scripts.count as htcount " Thanks On Wed, Aug 21, 2013 at 10:44 AM, Mahtab Mirmomeni < m.mirmom...@student.unimelb.edu.au> wrote: > You can use htseq_bams_to_count_matrix repository by fubar in the test > toolshed. > > > On Wed, Aug 21, 2013 at 2:37 PM, Sridhar Srinivasan < > sridhar2bioi...@gmail.com> wrote: > >> Hi All, >> >> Thanks for the suggestions. I installed the Toolshed ( Differential_Count >> (version 0.21) ). It asks for the input matrix - rows are contigs, columns >> are counts for each sample. >> Any idea on how to generate this matrix file?? >> >> Thanks >> >> >> On Tue, Aug 20, 2013 at 12:53 PM, Mahtab Mirmomeni < >> m.mirmom...@student.unimelb.edu.au> wrote: >> >>> Hi Sridhar, >>> >>> I'm using differential_count_model repository by fubar in the test >>> toolshed which has both EdgeR and Deseq2 and it's working for me. >>> >>> Thanks >>> Mahtab >>> >>> >>> On Tue, Aug 20, 2013 at 5:03 PM, Bjoern Gruening < >>> bjoern.gruen...@gmail.com> wrote: >>> >>>> Hi Sridhar, >>>> >>>> we are developing a DESeq2 tool at the moment, if you want to join get >>>> in touch with me. Its developed here: >>>> >>>> https://github.com/bgruening/galaxytools/tree/master/deseq2 >>>> >>>> I will upload our latest progress during the day. >>>> Cheers, >>>> Bjoern >>>> >>>> > Dear users, >>>> > >>>> > >>>> > Could anybody suggest the valid DESeq toolshed for RNA sequencing??? >>>> > >>>> > >>>> > Thanks >>>> > Sridhar >>>> > >>>> > ___ >>>> > 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/ >>>> >>>> >>>> >>>> ___ >>>> 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/ >>>> >>> >>> >> > ___ 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/
Re: [galaxy-dev] DESeq for Galaxy
Hi All, Thanks for the suggestions. I installed the Toolshed ( Differential_Count (version 0.21) ). It asks for the input matrix - rows are contigs, columns are counts for each sample. Any idea on how to generate this matrix file?? Thanks On Tue, Aug 20, 2013 at 12:53 PM, Mahtab Mirmomeni < m.mirmom...@student.unimelb.edu.au> wrote: > Hi Sridhar, > > I'm using differential_count_model repository by fubar in the test > toolshed which has both EdgeR and Deseq2 and it's working for me. > > Thanks > Mahtab > > > On Tue, Aug 20, 2013 at 5:03 PM, Bjoern Gruening < > bjoern.gruen...@gmail.com> wrote: > >> Hi Sridhar, >> >> we are developing a DESeq2 tool at the moment, if you want to join get >> in touch with me. Its developed here: >> >> https://github.com/bgruening/galaxytools/tree/master/deseq2 >> >> I will upload our latest progress during the day. >> Cheers, >> Bjoern >> >> > Dear users, >> > >> > >> > Could anybody suggest the valid DESeq toolshed for RNA sequencing??? >> > >> > >> > Thanks >> > Sridhar >> > >> > ___ >> > 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/ >> >> >> >> ___ >> 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/ >> > > ___ 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/
Re: [galaxy-dev] DESeq for Galaxy
Sure .. Thanks for the reply.. On Tue, Aug 20, 2013 at 12:33 PM, Bjoern Gruening wrote: > Hi Sridhar, > > we are developing a DESeq2 tool at the moment, if you want to join get > in touch with me. Its developed here: > > https://github.com/bgruening/galaxytools/tree/master/deseq2 > > I will upload our latest progress during the day. > Cheers, > Bjoern > > > Dear users, > > > > > > Could anybody suggest the valid DESeq toolshed for RNA sequencing??? > > > > > > Thanks > > Sridhar > > > > ___ > > 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/ > > > > ___ 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/
[galaxy-dev] DESeq for Galaxy
Dear users, Could anybody suggest the valid DESeq toolshed for RNA sequencing??? Thanks Sridhar ___ 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/
Re: [galaxy-dev] cummerBund installation
Dear Jermy, Thanks for the Toolshed link, I installed it in the galaxy and tried running it by choosing "build backend database using cuffdiff output" and added additional plot as Heatmap. The Job was run successfully but i could'nt view the HTML page.. it shows as "Galaxy - cummeRbund Output " below the filename i could see like" format: html, database: hg19 [1] "heatmap failed: Error in sqliteExecStatement(con, statement, bind.data): RS-DBI driver: (error in statement: near \")\": syntax error)\n" " The database created by cummeRbund is no way related to the initially created database "postgreSQL" ?? Your suggestions are very much Apperiacted... Thank you Sridhar On Fri, Jul 12, 2013 at 6:29 PM, Jeremy Goecks wrote: > The toolshed has a wrapper for cummerbund: > > http://toolshed.g2.bx.psu.edu/view/jjohnson/cummerbund > > On Jul 12, 2013, at 12:03 AM, sridhar srinivasan wrote: > > > Dear Developers, > > Could you please tell me the possibilities of using the R package > cummeRband for visualization of RNA-seq data in galaxy?? > > > Thanks > Sridhar > > ___ > 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/ > > > On Fri, Jul 12, 2013 at 6:29 PM, Jeremy Goecks wrote: > The toolshed has a wrapper for cummerbund: > > http://toolshed.g2.bx.psu.edu/view/jjohnson/cummerbund > > On Jul 12, 2013, at 12:03 AM, sridhar srinivasan wrote: > > > Dear Developers, > > Could you please tell me the possibilities of using the R package > cummeRband for visualization of RNA-seq data in galaxy?? > > > Thanks > Sridhar > > ___ > 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/ > > > ___ 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/
Re: [galaxy-dev] GATK
Thanks for the suggestin Linda... i removed the line -et "NO_ET" ##ET no phone home Now i am not getting the Error as get key to run the GATK.. But i am getting error as the fasta file is not found.. even in backend i found the command as mentioned below in the reference file section "-R " there is no link for the fasta file.. Please give the suggestion.. i mentioned many time this Error but i am not getting any reply.. python /illumina/data/galaxy/galaxy-dist/tools/gatk/gatk_wrapper.py --max_jvm_heap_fraction "1"--stdout "/illumina/data/galaxy/galaxy-dist/database/files/000/dataset_843.dat" -d "-I" "/illumina/data/galaxy/galaxy-dist/database/files/000/dataset_539.dat" "bam" "gatk_input_0"-d "" "/illumina/data/galaxy/galaxy-dist/database/files/_metadata_files/000/metadata_30.dat" "bam_index" "gatk_input_0" -p 'java -jar "/illumina/data/galaxy/galaxy-dist/tool-data/shared/jars/gatk/GenomeAnalysisTK.jar" -T "UnifiedGenotyper" --num_threads 4 --out "/illumina/data/galaxy/galaxy-dist/database/files/000/dataset_841.dat" --metrics_file "/illumina/data/galaxy/galaxy-dist/database/files/000/dataset_842.dat" * -R "" * --genotype_likelihoods_model "BOTH" --standard_min_confidence_threshold_for_calling "30.0" --standard_min_confidence_threshold_for_emitting "30.0"' Thanks Sridhar On Tue, Jun 11, 2013 at 1:01 PM, sridhar srinivasan < sridhar2bioi...@gmail.com> wrote: > Hello Linda, > Thanks for your suggestions. > > i removed the line from xml file but now i am getting different error. > > # ERROR > -- > > # ERROR A USER ERROR has occurred (version 2.5-2-gf57256b): > # ERROR The invalid arguments or inputs must be corrected before the GATK > can proceed > # ERROR Please do not post this error to the GATK forum > > # ERROR > # ERROR See the documentation (rerun with -h) for this tool to view > allowable command-line arguments. > # ERROR Visit our website and forum for extensive documentation and > answers to > # ERROR commonly asked questions http://www.broadinstitute.org/gatk > > # ERROR > # ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-sPZtN_) does > not exist. > # ERROR > -- > > I mentioned the path for human genome fasta file in .loc file , but again i > am getting same error. > > I am using GATK latest (GenomeAnalysisTK-2.5-2-gf57256b) version. > > > your suggestions are very much appericiated.. > > Thanks > Sridhar > > > > > > On Thu, Jun 6, 2013 at 5:23 PM, Linda Cham wrote: > >> Hi Sridhar, >> >> About the error, you need to request a key from GATK >> >> http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest >> See under "How to obtain and use a GATK key" >> >> Or by pass it by removing the -et "NO_ET" line from the xml files. >> >> >> >> [image: Inactive hide details for sridhar srinivasan ---06/06/2013 >> 06:30:48 AM---Dear Developers, I am running GATK for first time. In]sridhar >> srinivasan ---06/06/2013 06:30:48 AM---Dear Developers, I am running GATK >> for first time. In galaxy i use Unified Genotyper. I am >> >> From: sridhar srinivasan >> To: Galaxy Dev >> Date: 06/06/2013 06:30 AM >> Subject: [galaxy-dev] GATK >> Sent by: galaxy-dev-boun...@lists.bx.psu.edu >> -- >> >> >> >> Dear Developers, >> >> I am running GATK for first time. In galaxy i use Unified Genotyper. I am >> getting error as below mentioned. >> >> # ERROR >> -- >> >> # ERROR A USER ERROR has occurred (version 2.5-2-gf57256b): >> # ERROR The invalid arguments or inputs must be corrected before the >> GATK can proceed >> # ERROR Please do not post this error to the GATK forum >> >> # ERROR >> # ERROR See the documentation (rerun with -h) for this tool to view >> allowable command-line arguments. >> # ERROR Visit our website and forum for extensive documentation and >> answers to >> # ERROR commonly asked questions >> *http://www.broadinstitute.org/gatk*<http://www.broadinstitute.org/gatk> >> >> # ERRO
[galaxy-dev] GATK fasta file missing ERROR
Dear Developers, I am GATK (beta ) Unified Genotyper module to get the indels and SNP. I placed the jar file in (/galaxy-dist/tool-data/shared/jars/gatk) and i link the reference genome in .loc file (gatk_sorted_picard_index.loc). I could see the Name i mentioned in the .loc file is appearing in the galaxy page while choosing the Reference genome. Now while running GATK in galaxy , The command runs for a while and gives ERROR as i am getting ERROR as *(The fasta file you specified (/tmp/tmp-gatk-Jjg9Mi) does not exist.)* Could anybody suggest on the same.. Thanks Sridhar ___ 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/
Re: [galaxy-dev] Using Jar files in Galaxy
Hello Ross, Thanks for the reply.. i copied the source directory to tool-data/shared/jars now it works for the fastqc.. I tried the same for GATK copied the source directory t the location tool-data/shared/jars but it gives ERROR as mentioned below.. # ERROR -- # ERROR A USER ERROR has occurred (version 2.5-2-gf57256b): # ERROR The invalid arguments or inputs must be corrected before the GATK can proceed # ERROR Please do not post this error to the GATK forum # ERROR # ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. # ERROR Visit our website and forum for extensive documentation and answers to # ERROR commonly asked questions http://www.broadinstitute.org/gatk # ERROR # ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-EYMIaT) does not exist. # ERROR -- Could you please suggest on the same.. Thanks Sridhar On Fri, Jul 12, 2013 at 10:17 AM, Ross wrote: > Hi, Sridar, > > Why use the FastQC directory -tool-data/shared/jars would make it easy to > simply copy the way the current FastQC tool does this - the source for > FastQC xml and python wrappers are easy to find in the central repository > on bitbucket? > > However, to do it properly so it's easy to autoinstall from a tool shed, > please take a look at the test fastqc tool > http://testtoolshed.g2.bx.psu.edu/view/fubar/fastqc repository which > includes a tool_dependency.xml that autoinstalls the jar and sets up the > path for a properly managed dependency - avoiding the ugly solution found > in the existing fastqc tool. That's the way of the future for all tool > wrappers, so a good thing to start using. Plenty of docs on the wiki and > examples in the test toolshed. > > > On Fri, Jul 12, 2013 at 2:34 PM, sridhar srinivasan < > sridhar2bioi...@gmail.com> wrote: > >> Dear Developers, >> >> I am using java jar files for softwares like fastqc, GATK. For running >> these tools i install the softare and set path in bash_profile file. >> >> My doubt is i placed the jar files in galaxy dist folder ( >> >> galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc >> >> ) >> >> is this enough to call the jar files from galaxy?? >> >> After placing the jar file i tried running the tool using the interface >> it gives ERROR as >> >> # FastQC cl = >> /illumina/data/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc >> --outdir=/illumina/data/galaxy/galaxy-dist/database/job_working_directory/000/216/dataset_546_files >> --f=bam >> /illumina/data/galaxy/galaxy-dist/database/job_working_directory/000/216/dataset_546_files/Bowtie2_on_data_7_and_data_6__aligned_reads >> >> >> Exception in thread "main" java.lang.NoClassDefFoundError: >> uk/ac/babraham/FastQC/FastQCApplication >> >> Caused by: java.lang.ClassNotFoundException: >> uk.ac.babraham.FastQC.FastQCApplication >> >> at java.net.URLClassLoader$1.run(URLClassLoader.java:217) >> >> >> at java.security.AccessController.doPrivileged(Native Method) >> >> at java.net.URLClassLoader.findClass(URLClassLoader.java:205) >> >> at java.lang.ClassLoader.loadClass(ClassLoader.java:321) >> >> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) >> >> >> at java.lang.ClassLoader.loadClass(ClassLoader.java:266) >> >> Could not find the main class: uk.ac.babraham.FastQC.FastQCApplication. >> Program will exit. >> >> >> I got same error for GATK also >> >> # ERROR >> -- >> # ERROR A USER ERROR has occurred (version 2.5-2-gf57256b): >> # ERROR The invalid arguments or inputs must be corrected before the >> GATK can proceed >> >> >> # ERROR Please do not post this error to the GATK forum >> # ERROR >> # ERROR See the documentation (rerun with -h) for this tool to view >> allowable command-line arguments. >> # ERROR Visit our website and forum for extensive documentation and >> answers to >> >> >> # ERROR commonly asked questions http://www.broadinstitute.org/gatk >> # ERROR >> # ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-a3rr8t) >> does not exist. >> >> >> # ERROR >> --
[galaxy-dev] Using Jar files in Galaxy
Dear Developers, I am using java jar files for softwares like fastqc, GATK. For running these tools i install the softare and set path in bash_profile file. My doubt is i placed the jar files in galaxy dist folder ( galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc ) is this enough to call the jar files from galaxy?? After placing the jar file i tried running the tool using the interface it gives ERROR as # FastQC cl = /illumina/data/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/illumina/data/galaxy/galaxy-dist/database/job_working_directory/000/216/dataset_546_files --f=bam /illumina/data/galaxy/galaxy-dist/database/job_working_directory/000/216/dataset_546_files/Bowtie2_on_data_7_and_data_6__aligned_reads Exception in thread "main" java.lang.NoClassDefFoundError: uk/ac/babraham/FastQC/FastQCApplication Caused by: java.lang.ClassNotFoundException: uk.ac.babraham.FastQC.FastQCApplication at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:321) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:266) Could not find the main class: uk.ac.babraham.FastQC.FastQCApplication. Program will exit. I got same error for GATK also # ERROR -- # ERROR A USER ERROR has occurred (version 2.5-2-gf57256b): # ERROR The invalid arguments or inputs must be corrected before the GATK can proceed # ERROR Please do not post this error to the GATK forum # ERROR # ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. # ERROR Visit our website and forum for extensive documentation and answers to # ERROR commonly asked questions http://www.broadinstitute.org/gatk # ERROR # ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-a3rr8t) does not exist. # ERROR - Could you please suggest on the same.. Thanks Sridhar ___ 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/
[galaxy-dev] cummerBund installation
Dear Developers, Could you please tell me the possibilities of using the R package cummeRband for visualization of RNA-seq data in galaxy?? Thanks Sridhar ___ 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/
Re: [galaxy-dev] Visualization in galaxy
Hello Carl, Thanks for the reply. My file 9094 line its cuffdiff output.. After clicking the draw button it keep on shows rendering.. Thanks Sridhar On Thu, Jul 11, 2013 at 7:37 PM, Carl Eberhard wrote: > Hello, Sridhar > > How large is the file you're trying to plot? > > The scatterplot visualization doesn't do well with large datasets (more > than ~10,000 points). I'm working to provide some form of pagination, but > it may take some time. > > If your file is large, filtering or splitting up your data may help in the > meantime. > > If that doesn't help, can you provide more details as to what's happening > when you click the draw button? > > Thanks, > Carl > > > > On Thu, Jul 11, 2013 at 5:22 AM, sridhar srinivasan < > sridhar2bioi...@gmail.com> wrote: > >> Dear Developers, >> >> I could see the visualize icon in the History page below the output >> file.. Actually i am trying to plot the graph between the column 4 and 8 >> from the output.. >> >> I tried using the visualize option, But takes long time to and i could'nt >> get the plot.. >> >> Please suggest , how to get the Scatter plot >> >> >> >> your suggestions are very much appericiated.. >> >> >> Thanks >> Sridhar >> >> ___ >> 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/ >> > > ___ 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/
[galaxy-dev] Visualization in galaxy
Dear Developers, I could see the visualize icon in the History page below the output file.. Actually i am trying to plot the graph between the column 4 and 8 from the output.. I tried using the visualize option, But takes long time to and i could'nt get the plot.. Please suggest , how to get the Scatter plot your suggestions are very much appericiated.. Thanks Sridhar ___ 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/
[galaxy-dev] Fwd: GATK fasta file not found ERROR
Dear Developers, I am using GATK for first time. I am doing Targeted reseq Analysis. while i am running Unified Genotyper in Galaxy interface. it gives error message as mentioned below.. "ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-WBrGTf) does not exist." But i places the Fasta file path in .loc file(gatk_sorted_picard_index.loc). Also could anyone tell what are the preprocessing steps before using Bam file for Unified Genotyper?? Your answers are very much Appericiated. Thanks Sridhar ___ 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/
[galaxy-dev] GATK fasta file not found ERROR
Dear Developers, I am using GATK for first time. I am doing Targeted reseq Analysis. while i am running Unified Genotyper in Galaxy interface. it gives error message as mentioned below.. "ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-WBrGTf) does not exist." But i places the Fasta file path in .loc file. Also could anyone tell what are the preprocessing steps before using Bam file for Unified Genotyper?? Your answers are very much Appericiated. Thanks Sridhar ___ 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/
Re: [galaxy-dev] GATK
Hello Linda, Thanks for your suggestions. i removed the line from xml file but now i am getting different error. # ERROR -- # ERROR A USER ERROR has occurred (version 2.5-2-gf57256b): # ERROR The invalid arguments or inputs must be corrected before the GATK can proceed # ERROR Please do not post this error to the GATK forum # ERROR # ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. # ERROR Visit our website and forum for extensive documentation and answers to # ERROR commonly asked questions http://www.broadinstitute.org/gatk # ERROR # ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-sPZtN_) does not exist. # ERROR -- I mentioned the path for human genome fasta file in .loc file , but again i am getting same error. I am using GATK latest (GenomeAnalysisTK-2.5-2-gf57256b) version. your suggestions are very much appericiated.. Thanks Sridhar On Thu, Jun 6, 2013 at 5:23 PM, Linda Cham wrote: > Hi Sridhar, > > About the error, you need to request a key from GATK > > http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest > See under "How to obtain and use a GATK key" > > Or by pass it by removing the -et "NO_ET" line from the xml files. > > > > [image: Inactive hide details for sridhar srinivasan ---06/06/2013 > 06:30:48 AM---Dear Developers, I am running GATK for first time. In]sridhar > srinivasan ---06/06/2013 06:30:48 AM---Dear Developers, I am running GATK > for first time. In galaxy i use Unified Genotyper. I am > > From: sridhar srinivasan > To: Galaxy Dev > Date: 06/06/2013 06:30 AM > Subject: [galaxy-dev] GATK > Sent by: galaxy-dev-boun...@lists.bx.psu.edu > -- > > > > Dear Developers, > > I am running GATK for first time. In galaxy i use Unified Genotyper. I am > getting error as below mentioned. > > # ERROR > -- > > # ERROR A USER ERROR has occurred (version 2.5-2-gf57256b): > # ERROR The invalid arguments or inputs must be corrected before the > GATK can proceed > # ERROR Please do not post this error to the GATK forum > > # ERROR > # ERROR See the documentation (rerun with -h) for this tool to view > allowable command-line arguments. > # ERROR Visit our website and forum for extensive documentation and > answers to > # ERROR commonly asked questions > *http://www.broadinstitute.org/gatk*<http://www.broadinstitute.org/gatk> > > # ERROR > # ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option > requires a GATK Key file. Please see * > http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest > *<http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest> > for > more information and instructions on how to obtain a key. > > # ERROR > -- > > also suggest me about the Rod file for dbSNP. > > Thanks > > Sridhar___ > 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/ > <>___ 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/
[galaxy-dev] GATK
Dear Developers, I am running GATK for first time. In galaxy i use Unified Genotyper. I am getting error as below mentioned. # ERROR -- # ERROR A USER ERROR has occurred (version 2.5-2-gf57256b): # ERROR The invalid arguments or inputs must be corrected before the GATK can proceed # ERROR Please do not post this error to the GATK forum # ERROR # ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. # ERROR Visit our website and forum for extensive documentation and answers to # ERROR commonly asked questions http://www.broadinstitute.org/gatk # ERROR # ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option requires a GATK Key file. Please see http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest for more information and instructions on how to obtain a key. # ERROR -- also suggest me about the Rod file for dbSNP. Thanks Sridhar ___ 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/
[galaxy-dev] mapping Summary from Bowtie
Dear Developers, I am running Bowtie2 through galaxy interface, previously it gives the the mapping summary and convert the format to sam.. but now it directly convert the fastq file to bam and doesnt give the mapping summary. how to get the mapping summary from bowtie2 using galaxy interface.. Thanks Sridhar ___ 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/
[galaxy-dev] Genome not listed
Dear developers, 1. I recently installed galaxy locally. now i am trying to run bowtie2. In reference genome section the genome is not listed. 2. Is there any way yo secure our data without using the Proxy(nginx). I Appericiate your suggestions. Thanks Sridhar ___ 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/
Re: [galaxy-dev] Error in installing Galaxy.
Hello Rudolf, Thanks for the reply.. I use the command you mentioned in reply.. and the error is "psql: FATAL: Ident authentication failed for user "galaxy" " Thanks Sridhar On Tue, May 21, 2013 at 4:53 PM, Hans-Rudolf Hotz wrote: > Hi Sridhar > > Since we are using MySQL for our Galaxy server, I am kind of running out > of ideas...and hope someone else on the list can spot the error in your > universe.ini file. > > Just one last remark to double check: > > Can you log into the PostgreSQL database with the same credentials from > the command line? > > psql -d galaxy_prod -p 5432 -h localhost -U galaxy > > and this should prompt for the password > (again, I am not an PostgreSQL expert...) > > > Regards, Hans-Rudolf > > > > > On 05/21/2013 01:00 PM, sridhar srinivasan wrote: > >> Hello Rudolf, >> I tried with the IP address it gave the error as >> """ >> Is the server running on host "192.168.1.1" and accepting >> TCP/IP connections on port 5432? >> """ >> Then i try with 0.0.0.0 again i got same error >> >> OperationalError: (OperationalError) FATAL: Ident authentication failed >> for user "galaxy" >> None None >> >> Thanks >> Sridhar >> >> >> On Tue, May 21, 2013 at 3:08 PM, Hans-Rudolf Hotz > <mailto:h...@fmi.ch>> wrote: >> >> >> >> On 05/21/2013 11:22 AM, sridhar srinivasan wrote: >> >> Hi Rudolf, >> Thanks for the reply.. >> >> Could you please tell how to check and set the PostgreSQL .. >> I provide the correct username and password in universe.ini file.. >> >> when i give >> >> #database_connection = postgres:///galaxy_prod >> ?user=galaxy&password=password >> it gave error in history page >> """ >> Content Encoding Error >> >> >> The page you are trying to view cannot be shown because it uses an >> invalid or unsupported form of compression. >> >> * Please contact the website owners to inform them of >> this problem. >> >> """ >> >> >> Now after changing it into >> >> database_connection = >> postgres://galaxy:password@__**localhost:5432/galaxy_prod >> >> >> it gives error which i mentioned in previous mail >> >> Please suggest on this >> >> >> >> Assuming you replace 'password' with the actual password, the line >> looks correct to me. Try replacing 'localhost' with the IP address >> >> >> Regards, Hans-Rudolf >> >> >> >> >> Thanks >> Sridhar >> >> >> On Wed, May 8, 2013 at 7:16 PM, Hans-Rudolf Hotz > <mailto:h...@fmi.ch> >> <mailto:h...@fmi.ch <mailto:h...@fmi.ch>>> wrote: >> >> Hi Sridhar >> >> Have you set up your PostgreSQL database correctly? and >> provide the >> right username and password in the 'universe_wsgi.ini' file >> ? >> >> See: >> http://wiki.galaxyproject.org/**Admin/Config/Performance/_** >> ___ProductionServer?action=**show&redirect=Admin%** >> 2FConfig%2FPerformance#**Switching_to_a_database_**server >> <http://wiki.galaxyproject.**org/__Admin/Config/**Performance/__* >> *ProductionServer?action=show&_**_redirect=Admin%2FConfig%__** >> 2FPerformance#Switching_to_a__**_database_server> >> >> >> <http://wiki.galaxyproject.__**org/Admin/Config/Performance/_** >> _ProductionServer?action=show&**__redirect=Admin%2FConfig%__** >> 2FPerformance#Switching_to_a__**_database_server >> >> <http://wiki.galaxyproject.**org/Admin/Config/Performance/** >> ProductionServer?action=show&**redirect=Admin%2FConfig%** >> 2FPerformance#Switching_to_a_**database_server<http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=show&redirect=Admin%2FConfig%2FPerformance#Switching_to_a_database_server> >> >> >> >> Also, see this old thread, where the same error has been >> reported >> before: >> http://lists.bx.psu.edu/**pipermail/galaxy-dev/2010-May/** >> 002624.html<http://lists.bx
Re: [galaxy-dev] Error in installing Galaxy.
Hello Rudolf,
I tried with the IP address it gave the error as
"""
Is the server running on host "192.168.1.1" and accepting
TCP/IP connections on port 5432?
"""
Then i try with 0.0.0.0 again i got same error
OperationalError: (OperationalError) FATAL: Ident authentication failed
for user "galaxy"
None None
Thanks
Sridhar
On Tue, May 21, 2013 at 3:08 PM, Hans-Rudolf Hotz wrote:
>
>
> On 05/21/2013 11:22 AM, sridhar srinivasan wrote:
>
>> Hi Rudolf,
>> Thanks for the reply..
>>
>> Could you please tell how to check and set the PostgreSQL ..
>> I provide the correct username and password in universe.ini file..
>>
>> when i give
>>
>> #database_connection = postgres:///galaxy_prod
>> ?user=galaxy&password=password
>> it gave error in history page
>> """
>> Content Encoding Error
>>
>>
>> The page you are trying to view cannot be shown because it uses an
>> invalid or unsupported form of compression.
>>
>> * Please contact the website owners to inform them of this problem.
>>
>> """
>>
>>
>> Now after changing it into
>>
>> database_connection = postgres://galaxy:password@**
>> localhost:5432/galaxy_prod
>>
>> it gives error which i mentioned in previous mail
>>
>> Please suggest on this
>>
>
>
> Assuming you replace 'password' with the actual password, the line looks
> correct to me. Try replacing 'localhost' with the IP address
>
>
> Regards, Hans-Rudolf
>
>
>
>
>> Thanks
>> Sridhar
>>
>>
>> On Wed, May 8, 2013 at 7:16 PM, Hans-Rudolf Hotz > <mailto:h...@fmi.ch>> wrote:
>>
>> Hi Sridhar
>>
>> Have you set up your PostgreSQL database correctly? and provide the
>> right username and password in the 'universe_wsgi.ini' file ?
>>
>> See:
>> http://wiki.galaxyproject.org/**__Admin/Config/Performance/__**
>> ProductionServer?action=show&_**_redirect=Admin%2FConfig%__**
>> 2FPerformance#Switching_to_a__**_database_server
>>
>> <http://wiki.galaxyproject.**org/Admin/Config/Performance/**
>> ProductionServer?action=show&**redirect=Admin%2FConfig%**
>> 2FPerformance#Switching_to_a_**database_server<http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=show&redirect=Admin%2FConfig%2FPerformance#Switching_to_a_database_server>
>> >
>>
>> Also, see this old thread, where the same error has been reported
>> before:
>> http://lists.bx.psu.edu/__**pipermail/galaxy-dev/2010-May/**
>> __002624.html<http://lists.bx.psu.edu/__pipermail/galaxy-dev/2010-May/__002624.html><
>> http://lists.bx.psu.edu/**pipermail/galaxy-dev/2010-May/**002624.html<http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002624.html>
>> >
>>
>>
>>
>>
>> Regards, Hans-Rudolf
>>
>>
>>
>>
>> On 05/08/2013 01:24 PM, sridhar srinivasan wrote:
>>
>>
>> Hi ,
>>
>> I am getting error during Installing galaxy locally.
>>
>> Traceback (most recent call last):
>> File
>> "/illumina/apps/galaxy/galaxy-**__dist/lib/galaxy/webapps/__**
>> galaxy/buildapp.py",
>>
>> line 35, in app_factory
>> app = UniverseApplication( global_conf = global_conf,
>> **kwargs )
>> File
>> "/illumina/apps/galaxy/galaxy-**__dist/lib/galaxy/app.py", line
>> 51,
>>
>> in __init__
>> create_or_verify_database( db_url, kwargs.get(
>> 'global_conf', {}
>> ).get( '__file__', None ),
>> self.config.database_engine___**options, app=self )
>> File
>> "/illumina/apps/galaxy/galaxy-**__dist/lib/galaxy/model/**
>> migrate/__check.py",
>>
>> line 50, in create_or_verify_database
>> dataset_table = Table( "dataset", meta, autoload=True )
>> File
>> "/illumina/apps/galaxy/galaxy-**__dist/eggs/SQLAlchemy-0.5.6__**
>> _dev_r6498-py2.6.egg/__**sqlalchemy/schema.py",
>>
>> line 108, in __call__
>> return type.__call__(self, name, metadata, *args, **kwargs)
>> File
>> "/illumina/apps/galaxy/galaxy-**__dist/eggs/SQLAlchemy-0.5.6__**
>> _dev_r6498-
Re: [galaxy-dev] Error in installing Galaxy.
Hi Rudolf,
Thanks for the reply..
Could you please tell how to check and set the PostgreSQL ..
I provide the correct username and password in universe.ini file..
when i give
#database_connection = postgres:///galaxy_prod
?user=galaxy&password=password
it gave error in history page
"""
Content Encoding Error
The page you are trying to view cannot be shown because it uses an invalid
or unsupported form of compression.
* Please contact the website owners to inform them of this problem.
"""
Now after changing it into
database_connection = postgres://galaxy:password@localhost:5432/galaxy_prod
it gives error which i mentioned in previous mail
Please suggest on this
Thanks
Sridhar
On Wed, May 8, 2013 at 7:16 PM, Hans-Rudolf Hotz wrote:
> Hi Sridhar
>
> Have you set up your PostgreSQL database correctly? and provide the right
> username and password in the 'universe_wsgi.ini' file ?
>
> See: http://wiki.galaxyproject.org/**Admin/Config/Performance/**
> ProductionServer?action=show&**redirect=Admin%2FConfig%**
> 2FPerformance#Switching_to_a_**database_server<http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=show&redirect=Admin%2FConfig%2FPerformance#Switching_to_a_database_server>
>
> Also, see this old thread, where the same error has been reported before:
> http://lists.bx.psu.edu/**pipermail/galaxy-dev/2010-May/**002624.html<http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002624.html>
>
>
>
> Regards, Hans-Rudolf
>
>
>
>
> On 05/08/2013 01:24 PM, sridhar srinivasan wrote:
>
>>
>> Hi ,
>>
>> I am getting error during Installing galaxy locally.
>>
>> Traceback (most recent call last):
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/lib/galaxy/webapps/**
>> galaxy/buildapp.py",
>> line 35, in app_factory
>> app = UniverseApplication( global_conf = global_conf, **kwargs )
>>File "/illumina/apps/galaxy/galaxy-**dist/lib/galaxy/app.py", line 51,
>> in __init__
>> create_or_verify_database( db_url, kwargs.get( 'global_conf', {}
>> ).get( '__file__', None ), self.config.database_engine_**options,
>> app=self )
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/lib/galaxy/model/migrate/**
>> check.py",
>> line 50, in create_or_verify_database
>> dataset_table = Table( "dataset", meta, autoload=True )
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/eggs/SQLAlchemy-0.5.6_**
>> dev_r6498-py2.6.egg/**sqlalchemy/schema.py",
>> line 108, in __call__
>> return type.__call__(self, name, metadata, *args, **kwargs)
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/eggs/SQLAlchemy-0.5.6_**
>> dev_r6498-py2.6.egg/**sqlalchemy/schema.py",
>> line 236, in __init__
>> _bind_or_error(metadata).**reflecttable(self,
>> include_columns=include_**columns)
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/eggs/SQLAlchemy-0.5.6_**
>> dev_r6498-py2.6.egg/**sqlalchemy/engine/base.py",
>> line 1261, in reflecttable
>> conn = self.contextual_connect()
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/eggs/SQLAlchemy-0.5.6_**
>> dev_r6498-py2.6.egg/**sqlalchemy/engine/base.py",
>> line 1229, in contextual_connect
>> return self.Connection(self, self.pool.connect(),
>> close_with_result=close_with_**result, **kwargs)
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/eggs/SQLAlchemy-0.5.6_**
>> dev_r6498-py2.6.egg/**sqlalchemy/pool.py",
>> line 142, in connect
>> return _ConnectionFairy(self).**checkout()
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/eggs/SQLAlchemy-0.5.6_**
>> dev_r6498-py2.6.egg/**sqlalchemy/pool.py",
>> line 304, in __init__
>> rec = self._connection_record = pool.get()
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/eggs/SQLAlchemy-0.5.6_**
>> dev_r6498-py2.6.egg/**sqlalchemy/pool.py",
>> line 161, in get
>> return self.do_get()
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/eggs/SQLAlchemy-0.5.6_**
>> dev_r6498-py2.6.egg/**sqlalchemy/pool.py",
>> line 639, in do_get
>> con = self.create_connection()
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/eggs/SQLAlchemy-0.5.6_**
>> dev_r6498-py2.6.egg/**sqlalchemy/pool.py",
>> line 122, in create_connection
>> return _ConnectionRecord(self)
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/eggs/SQLAlchemy-0.5.6_**
>> dev_r6498-py2.6
[galaxy-dev] Web Page Problem
Dear Developers,
After installing galaxy, the history part of the webpage is not opening and
it shows
" Content Encoding Error
The page you are trying to view cannot be shown because it uses an invalid
or unsupported form of compression.
* Please contact the website owners to inform them of this problem."
when i try to reload in backend i am getting this message..
Exception happened during processing of request from ('192.168.1.6', 55016)
Traceback (most recent call last):
File
"/illumina/apps/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py",
line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File "/usr/lib64/python2.6/SocketServer.py", line 322, in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib64/python2.6/SocketServer.py", line 618, in __init__
self.finish()
File "/usr/lib64/python2.6/SocketServer.py", line 661, in finish
self.wfile.flush()
File "/usr/lib64/python2.6/socket.py", line 303, in flush
self._sock.sendall(buffer(data, write_offset, buffer_size))
error: [Errno 32] Broken pipe
Could anybody suggest on this issue...
Thanks
Sridhar
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[galaxy-dev] Fwd: History page not opening
Hi, In backend i am getting this message 192.168.1.5 - - [15/May/2013:09:32:12 +0600] "GET / HTTP/1.1" 200 - "http://192.168.1.5- -/" "Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.9.2.18) Gecko/20110616 Red Hat/3.6-1.el5_6 Firefox/3.6.18" Thanks Sridhar On 5/14/13, sridhar srinivasan wrote: > Hi Carl, > > I am using firefox 3.6.18 and linux Red Hat/3.6-1.el5_6.. > > Thanks > Sridhar > > > On Mon, May 13, 2013 at 8:31 PM, Carl Eberhard > wrote: > >> Hello, Sridhar. >> >> Can you tell me the browser and operating system you're using? >> >> Thanks, >> Carl >> >> >> >> On Mon, May 13, 2013 at 6:50 AM, sridhar srinivasan < >> sridhar2bioi...@gmail.com> wrote: >> >>> Hi after installing galaxy, >>> i could'nt see the history page in right end of galaxy web. >>> it shows >>> >>> """ >>> Content Encoding Error >>> >>> >>> The page you are trying to view cannot be shown because it uses an >>> invalid or unsupported form of compression. >>> >>> * Please contact the website owners to inform them of this >>> problem. >>> >>> """ >>> >>> Please help me to solve the issue.. >>> >>> sridhar >>> >>> ___ >>> 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/ >>> >> >> > ___ 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/
Re: [galaxy-dev] History page not opening
Hi Carl, I am using firefox 3.6.18 and linux Red Hat/3.6-1.el5_6.. Thanks Sridhar On Mon, May 13, 2013 at 8:31 PM, Carl Eberhard wrote: > Hello, Sridhar. > > Can you tell me the browser and operating system you're using? > > Thanks, > Carl > > > > On Mon, May 13, 2013 at 6:50 AM, sridhar srinivasan < > sridhar2bioi...@gmail.com> wrote: > >> Hi after installing galaxy, >> i could'nt see the history page in right end of galaxy web. >> it shows >> >> """ >> Content Encoding Error >> >> >> The page you are trying to view cannot be shown because it uses an >> invalid or unsupported form of compression. >> >> * Please contact the website owners to inform them of this problem. >> >> """ >> >> Please help me to solve the issue.. >> >> sridhar >> >> ___ >> 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/ >> > > ___ 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/
Re: [galaxy-dev] history page not opening
Hi, I am using Nginx proxy server for it. Also i followed jim vallandingham steps for installation of galaxy locally.. http://vallandingham.me/galaxy_install.html Thanks Sridhar On Mon, May 13, 2013 at 11:10 PM, James Taylor wrote: > How is your Galaxy configured? Are you using any kind of proxy server > in front of it? > > -- > James Taylor, Assistant Professor, Biology/CS, Emory University > > > On Mon, May 13, 2013 at 2:53 AM, sridhar srinivasan > wrote: > > Dear Developers, > > > > After configuring the galaxy.. i could'nt see the history column in the > web > > page.. > > it shows the error as > > > > "Content Encoding Error > > The page you are trying to view cannot be shown because it uses an > invalid > > or unsupported form of compression." > > > > > > Best > > Sridhar > > > > ___ > > 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/ > ___ 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/
[galaxy-dev] History page not opening
Hi after installing galaxy, i could'nt see the history page in right end of galaxy web. it shows """ Content Encoding Error The page you are trying to view cannot be shown because it uses an invalid or unsupported form of compression. * Please contact the website owners to inform them of this problem. """ Please help me to solve the issue.. sridhar ___ 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/
[galaxy-dev] history page not opening
Dear Developers, After configuring the galaxy.. i could'nt see the history column in the web page.. it shows the error as "Content Encoding Error The page you are trying to view cannot be shown because it uses an invalid or unsupported form of compression." Best Sridhar ___ 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/
Re: [galaxy-dev] Error in installing Galaxy.
Thanks for the reply.. Yeah i am using the Host=0.0.0.0 but i couldn't connect.. now after installing ngnix and reloading i am getting error like.. Traceback (most recent call last): File "./scripts/paster.py", line 33, in serve.run() File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1056, in run invoke(command, command_name, options, args[1:]) File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1062, in invoke exit_code = runner.run(args) File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 227, in run result = self.command() File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 677, in command serve() File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 661, in serve server(app) File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 292, in server_wrapper **context.local_conf) File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 97, in fix_call val = callable(*args, **kw) File "/illumina/apps/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1342, in server_runner serve(wsgi_app, **kwargs) File "/illumina/apps/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1291, in serve request_queue_size=request_queue_size) File "/illumina/apps/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1134, in __init__ request_queue_size=request_queue_size) File "/illumina/apps/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1113, in __init__ request_queue_size=request_queue_size) File "/illumina/apps/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 328, in __init__ HTTPServer.__init__(self, server_address, RequestHandlerClass) File "/usr/lib64/python2.6/SocketServer.py", line 402, in __init__ self.server_bind() File "/usr/lib64/python2.6/BaseHTTPServer.py", line 108, in server_bind SocketServer.TCPServer.server_bind(self) File "/usr/lib64/python2.6/SocketServer.py", line 413, in server_bind self.socket.bind(self.server_address) File "", line 1, in bind socket.error: [Errno 98] Address already in use galaxy.jobs.handler INFO 2013-05-10 10:22:14,360 sending stop signal to worker thread galaxy.jobs.handler INFO 2013-05-10 10:22:14,360 job handler queue stopped galaxy.jobs.runners INFO 2013-05-10 10:22:14,360 LWRRunner: Sending stop signal to monitor thread galaxy.jobs.runners INFO 2013-05-10 10:22:14,360 LWRRunner: Sending stop signal to 3 worker threads galaxy.jobs.runners INFO 2013-05-10 10:22:14,360 LocalRunner: Sending stop signal to 5 worker threads galaxy.jobs.handler INFO 2013-05-10 10:22:14,362 sending stop signal to worker thread galaxy.jobs.handler INFO 2013-05-10 10:22:14,362 job handler stop queue stopped Exception in thread LWRRunner.monitor_thread (most likely raised during interpreter shutdown):Exception in thread JobHandlerQueue.monitor_thread (most likely raised during interpreter shutdown): Traceback (most recent call last): Traceback (most recent call last): On Thu, May 9, 2013 at 5:15 PM, Dannon Baker wrote: > On Thu, May 9, 2013 at 12:21 AM, sridhar srinivasan < > sridhar2bioi...@gmail.com> wrote: > >> and it is working.. but i could'nt connect to the webpage >> http://127.0.0.1:8080/ from another system in same network.. >> >> > By default, galaxy will only be serving on 127.0.0.1 (localhost), which is > a loopback and only accessible on the machine itself. Accessing 127.0.0.1 > using another machine on the network is actually making requests to the > machine you're trying that from, which I assume isn't running galaxy. > > In your universe_wsgi.ini, you can edit this via the 'host' setting. Just > use 0.0.0.0 to listen to all connections. > > -Dannon > ___ 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/
Re: [galaxy-dev] Error in installing Galaxy.
Hi Rudolf,
Thanks for the reply.
Previously i was using the
postgres://user:pass@host/galaxy in 'universe_wsgi.ini'
now i tried with
postgres:///
and it is working.. but i could'nt connect to the webpage
http://127.0.0.1:8080/ from another system in same network..
Sridhar
On Wed, May 8, 2013 at 7:16 PM, Hans-Rudolf Hotz wrote:
> Hi Sridhar
>
> Have you set up your PostgreSQL database correctly? and provide the right
> username and password in the 'universe_wsgi.ini' file ?
>
> See: http://wiki.galaxyproject.org/**Admin/Config/Performance/**
> ProductionServer?action=show&**redirect=Admin%2FConfig%**
> 2FPerformance#Switching_to_a_**database_server<http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=show&redirect=Admin%2FConfig%2FPerformance#Switching_to_a_database_server>
>
> Also, see this old thread, where the same error has been reported before:
> http://lists.bx.psu.edu/**pipermail/galaxy-dev/2010-May/**002624.html<http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002624.html>
>
>
>
> Regards, Hans-Rudolf
>
>
>
>
> On 05/08/2013 01:24 PM, sridhar srinivasan wrote:
>
>>
>> Hi ,
>>
>> I am getting error during Installing galaxy locally.
>>
>> Traceback (most recent call last):
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/lib/galaxy/webapps/**
>> galaxy/buildapp.py",
>> line 35, in app_factory
>> app = UniverseApplication( global_conf = global_conf, **kwargs )
>>File "/illumina/apps/galaxy/galaxy-**dist/lib/galaxy/app.py", line 51,
>> in __init__
>> create_or_verify_database( db_url, kwargs.get( 'global_conf', {}
>> ).get( '__file__', None ), self.config.database_engine_**options,
>> app=self )
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/lib/galaxy/model/migrate/**
>> check.py",
>> line 50, in create_or_verify_database
>> dataset_table = Table( "dataset", meta, autoload=True )
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/eggs/SQLAlchemy-0.5.6_**
>> dev_r6498-py2.6.egg/**sqlalchemy/schema.py",
>> line 108, in __call__
>> return type.__call__(self, name, metadata, *args, **kwargs)
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/eggs/SQLAlchemy-0.5.6_**
>> dev_r6498-py2.6.egg/**sqlalchemy/schema.py",
>> line 236, in __init__
>> _bind_or_error(metadata).**reflecttable(self,
>> include_columns=include_**columns)
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/eggs/SQLAlchemy-0.5.6_**
>> dev_r6498-py2.6.egg/**sqlalchemy/engine/base.py",
>> line 1261, in reflecttable
>> conn = self.contextual_connect()
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/eggs/SQLAlchemy-0.5.6_**
>> dev_r6498-py2.6.egg/**sqlalchemy/engine/base.py",
>> line 1229, in contextual_connect
>> return self.Connection(self, self.pool.connect(),
>> close_with_result=close_with_**result, **kwargs)
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/eggs/SQLAlchemy-0.5.6_**
>> dev_r6498-py2.6.egg/**sqlalchemy/pool.py",
>> line 142, in connect
>> return _ConnectionFairy(self).**checkout()
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/eggs/SQLAlchemy-0.5.6_**
>> dev_r6498-py2.6.egg/**sqlalchemy/pool.py",
>> line 304, in __init__
>> rec = self._connection_record = pool.get()
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/eggs/SQLAlchemy-0.5.6_**
>> dev_r6498-py2.6.egg/**sqlalchemy/pool.py",
>> line 161, in get
>> return self.do_get()
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/eggs/SQLAlchemy-0.5.6_**
>> dev_r6498-py2.6.egg/**sqlalchemy/pool.py",
>> line 639, in do_get
>> con = self.create_connection()
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/eggs/SQLAlchemy-0.5.6_**
>> dev_r6498-py2.6.egg/**sqlalchemy/pool.py",
>> line 122, in create_connection
>> return _ConnectionRecord(self)
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/eggs/SQLAlchemy-0.5.6_**
>> dev_r6498-py2.6.egg/**sqlalchemy/pool.py",
>> line 198, in __init__
>> self.connection = self.__connect()
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/eggs/SQLAlchemy-0.5.6_**
>> dev_r6498-py2.6.egg/**sqlalchemy/pool.py",
>> line 261, in __connect
>> connection = self.__pool._creator()
>>File
>> "/illumina/apps/galaxy/galaxy-**dist/eggs/SQLAlchemy-0.5.6_**
>> de
[galaxy-dev] Error in installing Galaxy.
Hi ,
I am getting error during Installing galaxy locally.
Traceback (most recent call last):
File
"/illumina/apps/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py",
line 35, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/app.py", line 51, in
__init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options, app=self )
File
"/illumina/apps/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line
50, in create_or_verify_database
dataset_table = Table( "dataset", meta, autoload=True )
File
"/illumina/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py",
line 108, in __call__
return type.__call__(self, name, metadata, *args, **kwargs)
File
"/illumina/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py",
line 236, in __init__
_bind_or_error(metadata).reflecttable(self,
include_columns=include_columns)
File
"/illumina/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
line 1261, in reflecttable
conn = self.contextual_connect()
File
"/illumina/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
line 1229, in contextual_connect
return self.Connection(self, self.pool.connect(),
close_with_result=close_with_result, **kwargs)
File
"/illumina/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py",
line 142, in connect
return _ConnectionFairy(self).checkout()
File
"/illumina/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py",
line 304, in __init__
rec = self._connection_record = pool.get()
File
"/illumina/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py",
line 161, in get
return self.do_get()
File
"/illumina/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py",
line 639, in do_get
con = self.create_connection()
File
"/illumina/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py",
line 122, in create_connection
return _ConnectionRecord(self)
File
"/illumina/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py",
line 198, in __init__
self.connection = self.__connect()
File
"/illumina/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py",
line 261, in __connect
connection = self.__pool._creator()
File
"/illumina/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/strategies.py",
line 80, in connect
raise exc.DBAPIError.instance(None, None, e)
OperationalError: (OperationalError) FATAL: Ident authentication failed
for user "galaxy"
None None
I created a user galaxy to install galaxy locally.
Thanks in Advance.
Sridhar
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Re: [galaxy-dev] (no subject)
HI, Thanks for the reply. actually my server is not connected with the internet. Previously i downloaded in another system with internet connection and installed to server. now i gave internet connection to the server now i could connect to it and download the python eggs. Thanks Sridhar On Sat, May 4, 2013 at 12:36 AM, Adam Brenner wrote: > > What version of Python are you using? I believe Python 2.7 is the > recommend version. I suggest you grab a fresh copy of galaxy from the > stable branch and try again. > > -- > Adam Brenner > Computer Science, Undergraduate Student > Donald Bren School of Information and Computer Sciences > > Research Computing Support > Office of Information Technology > http://www.oit.uci.edu/rcs/ > > University of California, Irvine > www.ics.uci.edu/~aebrenne/ <http://www.ics.uci.edu/%7Eaebrenne/> > aebre...@uci.edu > > > On Fri, May 3, 2013 at 12:24 AM, sridhar srinivasan < > sridhar2bioi...@gmail.com> wrote: > >> Dear All, >> >> i am installing galaxy first time. >> >> i face problem while installing the python eggs. >> while running the Run.sh command it gives as >> >> /home/sbsuser/.python-eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg-tmp/csamtools.so:6: >> RuntimeWarning: __builtin__.file size changed, may indicate binary >> incompatibility >> � b �n 64 0� c � � � �� ? �� � ��U �#k � ! \ j Z o� [ & � � � [ < >> � � �9 - �� ra # ��� �� 8n � �C �U�; B � S l K (p� �� U � & � P w 5 ≠ >> ' H š è π ø * ─ ␋ Ð Ä @ ê >> >> >> i couldn't read the message and also i couldn't open the galaxy page >> >> http://localhost:8080 >> >> >> Could you please suggest tth epossibilities to install. >> >> >> Thanks in advance >> >> Regards >> Sridhar >> >> >> ___ >> 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/ >> > > ___ 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/
[galaxy-dev] (no subject)
Dear All, i am installing galaxy first time. i face problem while installing the python eggs. while running the Run.sh command it gives as /home/sbsuser/.python-eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg-tmp/csamtools.so:6: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility �b�n 640�c�����?�����U�#k�!\jZo�[&� ��[<���9-��ra#����� 8n��C�U�;B�SlK(p���U�&�P w 5 ≠ ' H è π ø * ─ ␋ Ð Ä @ ê i couldn't read the message and also i couldn't open the galaxy page http://localhost:8080 Could you please suggest tth epossibilities to install. Thanks in advance Regards Sridhar ___ 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/
