Re: [galaxy-dev] tool for STAR RNA-seq aligner
Hi all, I do have a version 0.1 wrapper for STAR under our oqtans package, however it is not yet in toolshed. https://github.com/ratschlab/oqtans_tools/tree/master/STAR/2.3/ Feel free to comment, Vipin | Rätsch Lab On Wed, Sep 24, 2014 at 4:55 PM, Curtis Hendrickson (Campus) curt...@uab.edu wrote: Bjorn We'd be interested in this tool, as well. Any idea how close to functional it is? I see it's only on TEST toolshed, and not on production, at this point. I don't see any related Trello card when searching on star Regards, Curtis Galaxy Admin @ University of Alabama at Birmingham -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto: galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Björn Grüning Sent: Wednesday, September 24, 2014 3:15 PM To: galaxy-dev@lists.bx.psu.edu; hoove...@helix.nih.gov David Hoover Subject: Re: [galaxy-dev] tool for STAR RNA-seq aligner Hi David, yes there is inital code in the https://testtoolshed.g2.bx.psu.edu/. I think Ross has done some work on it. The main problem with Star is that is needs special indices (and a lot of it) and it would be great to offer data managers for it. Cheers, Bjoern Am 24.09.2014 um 22:05 schrieb David Hoover: Hi, I am developing a tool for STAR (https://code.google.com/p/rna-star/), and I realize I may be reinventing another wheel. Has anyone else created a tool for STAR? There's nothing else in the toolsheds for it yet. David David Hoover, PhD Helix Systems Staff SCB/DCSS/CIT/NIH 301-435-2986 http://helix.nih.gov ___ 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/ ___ 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 while installing DESeq-hts
Hey Greet and Bjoern,
Sorry for the troubles with dependencies during the automated installation
procedure!
I will add tool dependency file, when I get some time during this weekend
:)
Vipin | Rätsch Lab
On Tue, Jul 29, 2014 at 10:06 AM, Björn Grüning bjoern.gruen...@gmail.com
wrote:
Hi Geert and Vipin,
I might also consider the DESeq package and the wrappers from galaxytools
if you plan to update your wrappers.
https://github.com/bgruening/galaxytools/tree/master/
orphan_tool_dependencies/package_deseq2_1_2_10
@Geert: impressive documentation! Thanks a lot for sharing!
Bjoern
Am 29.07.2014 um 15:54 schrieb Geert Vandeweyer:
I know this is a very old entry to the mailing list, but I thought this
might be useful for some people.
Recently, I set up DESeq-hts and its siblings on our galaxy instance. To
succeed, I performed the steps below.
@vipin: would you consider revising the tool_dependencies.xml for these
tools to take these steps into account? If you're interested, I might
compose a preliminary version. I believe that most, if not all of these
settings can be automated using the tool_dependencies files.
I did not manage to get DEXSeq working, as it throws errors on the
'estimateDispersions' step in R. I'm not sure how to solve this, as it
gives me the same errors using the demonstration data from the pasilla
library, following the manual steps. (R 3.0.2, bioconductor 2.13, DEXSeq
1.8). Any hints on that are welcome.
Best,
Geert
## GALAXY PACKAGES IN TOOLSHED
###
- install the DESeq-hts tools from the main toolshed (cec4b4fb30be from
vipints)
- install R into galaxy (I used package_R_3_0_2 from iuc (50f7e1e71271))
- install package_scipi and package_numpi (from iuc)
- install package_samtools-0.1.18 (I used
devteam/package_samtools_0_1_18/c0f72bdba484)
- install htseq_count package (I used d5edaf8dc974 from lparsons)
## INSTALL DESeq bioconductor package
#
- open R from the commandline (using the R version installed earlier !),
install bioconductor package 'DESeq' :
- source(http://bioconductor.org/biocLite.R;)
- biocLite('DESeq')
- biocLite('DESeq2')
- biocLite('DEXSeq') (needed extra ubuntu package
libcurl4-gnutls-dev for this)
## complie samtools from source (temporary)
#
- download samtools 0.1.18 source code into a temporary location and
unpack
- compile with : make CXXFLAGS=-fPIC CFLAGS=-fPIC CPPFLAGS=-fPIC
## install octave
###
- OS-dependent, ubuntu: apt-get install octave
## set up DESeq-hts-1.0
###
- go to
/path_to_shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/
deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_1.0
- run : setup_deseq-hts.sh and provide paths as requested.
- NOTE: set samtools path to the source compiled version for now
(shed version fails to find sam.h)!!
- NOTE: also add NumPy path to the SCIPY_PATH variable
- rest: example (available in bin/deseq_config.sh):
export LD_LIBRARY_PATH=
export ENVIRONMENT=galaxy
export DESEQ_VERSION=1.12.1
export
DESEQ_PATH=/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/
vipints/deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_1.0
export
DESEQ_SRC_PATH=/galaxy/shed_tools/toolshed.g2.bx.psu.edu/
repos/vipints/deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_1.0/src
export
DESEQ_BIN_PATH=/galaxy/shed_tools/toolshed.g2.bx.psu.edu/
repos/vipints/deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_1.0/bin
export INTERPRETER=octave
export MATLAB_BIN_PATH=
export MATLAB_MEX_PATH=
export MATLAB_INCLUDE_DIR=
export OCTAVE_BIN_PATH=/opt/software/octave-3.8.0/bin/octave
export OCTAVE_MKOCT=/opt/software/octave-3.8.0/bin/mkoctfile
export SAMTOOLS_DIR=/galaxy/packages_
sources/samtools-0.1.18_fPIC
#export
SAMTOOLS_DIR=/galaxy/galaxy_tool_binaries/samtools/0.1.18/
devteam/package_samtools_0_1_18/c0f72bdba484/bin/
export PYTHON_PATH=/galaxy/galaxy_env/bin/python
export
SCIPY_PATH=/galaxy/galaxy_tool_binaries/scipy/0.12.0/
iuc/package_scipy_0_12/984d208b0808/lib/python/:/
galaxy/galaxy_tool_binaries/numpy/1.7.1/iuc/package_numpy_
1_7/ef12a3a11d5b/lib/python/
## USE THE TOOLSHED VERSION, The one you installed bioclite
packages with.
export
R_PATH=/galaxy/galaxy_tool_binaries/R_3_0_2/3.0.2/iuc/
package_r_3_0_2/50f7e1e71271/R
- enter mex directory, run make octave
- swap SAMTOOLS_DIR in bin/deseq_config.sh to point to the toolshed
version of samtools 0.1.18
## RUN DESeq-hts-1.0 TEST
##
enter src directory, run test from the toolconf xml file:
./deseq-hts.sh ../test_data/deseq_c_elegans_WS200-I-regions.gff3
../test_data/deseq_c_elegans_WS200-I-regions_deseq.txt
../test_data/genes.mat
../test_data/deseq_c_elegans_WS200-I-regions-SRX001872.bam
[galaxy-dev] Toolshed upload error message
Hi Greg, When I trying to upload a next release version o my https://toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf converter program to Community Toolshed, I am getting an internal error message. I am uploading a tar.gz file to the page https://toolshed.g2.bx.psu.edu/ but this fails. Could you please pass the error message or let me how I can add new files to the repository and delete the old version. Thanks, Vipin | Rätsch Lab ___ 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] Galaxy customized tool config file
Thanks Bj örn! for pointing the right issue card, I uplifted those. Vipin On Wed, Jun 4, 2014 at 12:45 PM, Bj örn Grüning bjoern.gruen...@gmail.com wrote: Hi Vipin, that is currently not possible but a high priority of the Galaxy deavteam. You can follow the status in several trello cards: https://trello.com/c/VizlCET9 https://trello.com/c/phMelslw Ciao, Bjoern Am 04.06.2014 18:33, schrieb Vipin TS: Sorry for re-posting! any suggestions to make an interactive tool page. Thanks you, Vipin On Tue, May 20, 2014 at 5:25 PM, Vipin TS vipin...@gmail.com wrote: Hello dev-team, With the current state, is it possible to write an interactive page for a tool in Galaxy? In my case, I m considering to build a tool page with JavaScript embed in XML file, my expectation is to behave the Galaxy tool page as google translate page with option instant translation on (display the same text content in the next box). I have checked the Admin/Tools/ToolConfigSyntax, not sure whether I missed anything related this. any comments ? thanks, Vipin galaxy.cbio.mskcc.org ___ 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/
[galaxy-dev] Galaxy customized tool config file
Hello dev-team, With the current state, is it possible to write an interactive page for a tool in Galaxy? In my case, I m considering to build a tool page with JavaScript embed in XML file, my expectation is to behave the Galaxy tool page as google translate page with option instant translation on (display the same text content in the next box). I have checked the Admin/Tools/ToolConfigSyntax, not sure whether I missed anything related this. any comments ? thanks, Vipin galaxy.cbio.mskcc.org ___ 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] tool_sheds_errors
On Thu, Mar 13, 2014 at 5:32 PM, Wang, Xiaofei xfw...@ku.edu wrote: Hi Folks, I figured out the problem of tool dependencies successfully. The installation status is installed for all tool sheds. The tools are also shown on left tool panel. But, I got problems when I used the tool sheds to analyze data. For example, When I used GFF-TO-BED (fml_gff3togtf), the error is: python: can't open file '~/softwares/shed_tools/ toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf/ed53dca1c6ff/fml_gff3togtf/fml_gff_converter_programs /galaxy/bed_to_gff3_converter.py': [Errno 2] No such file or directory When I checked the ~/.../galaxy folder, there are four *.xml files. Then, I copied the four files from ~/.../script folder. Now, this tool works. But, I don't think this is a right way to figure out this because I also got similar problem (I think they are similar) when I used other tool sheds as below. So, I am guessing it might be a problem with my configure file (universe_wsgi.ini). Could anybody tell me why and how to figure it out? Hello, I am responsible for answering the first part of your error message, It is my mistake that I have to place the right path in the tool configuration file (xml). This will be fixed soon and update the repository to a new version. regards, Vipin | Rätsch Lab BWA wrapper error: when I used the BWA wrapper for Illunina, An error occurred with this dataset: Could not determine BWA version Error indexing reference sequence. /bin/sh: bwa: command not found I referred to this link to try to figure out the problem http://osdir.com/ml/galaxy-development-source-control/2011-10/msg00268.html. But, I think I need more details about the mentioned bwa binaries and path. When I used the snpEff, the error is: Unable to access jarfile /Users/pablocingolani/snpEff/snpEff.jar In fact, the snpEff.jar is located at ~/softwares/shed_tools/ toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/c052639fa666/snpeff/snpEff_2_1a/snpEff_2_1a Could you give me some ideas? Thank you so much! ___ 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] dynamic select problem
filter type=param_value ref=inputmodel column=2/ filter type=param_value ref=inputSize column=3/ If you closely look at the above line the double quotes are different for column field. filter type=param_value ref=inputRealization column=4 / /options /param Did you figure out where the problem is? Thanks, Saba ___ 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] Converting .gff3 to 12-column .bed
Hi, I am the author for fml_gff3togtf tool package, currently merged into our instance at http://galaxy.cbio.mskcc.org, The tool can be accessed with following link: https://galaxy.cbio.mskcc.org/tool_runner?tool_id=fml_gff2bed --/Vipin Sloan-Kettering Institute http://galaxy.cbio.mskcc.org On Mon, Nov 11, 2013 at 12:15 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hello, There are no tools directly on the public Galaxy site to transform a GFF3 dataset into a BED12 dataset. However, the Tool Shed has a repository called ' fml_gff3togtf' that includes a tool for this purpose, for use in a local install. The description is a bit bothersome in that it a slightly incorrect datatype statement, so be sure to test out the results. (the word wiggle has no place in this statement: gff3_to_bed_converter.py: This tool converts gene transcript annotation from GFF3 format to UCSC wiggle 12 column BED format.) http://getgalaxy.org http://usegalaxy.org/toolshed I see your post at Biostar, and it might be helpful to let you know what a BED12 file represents (plus I'll post this there, may help others): http://www.biostars.org/p/85869/ A BED12 file describes the complete, often spliced, alignment of a sequence to a reference genome. This does not include minor base variation, it is a macro alignment. You can think of each of the blocks as being exons, although there is no magic here - if the sequence or genome had quality problems, or significant variation (large insertion or deletion), that could cause the alignment to fragment as well. Here is the data description: http://wiki.galaxyproject.org/Learn/Datatypes#Bed To see examples, at UCSC (genome.ucsc.edu), EST or mRNA track will have this as the primary table format. All gene track can also be in BED12 format, or in a related one, genePred: http://genome.ucsc.edu/FAQ/FAQformat.html#format9 UCSC also has line-command utilities to convert between the formats, pre-compiled versions are here: http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads Either way, you can convert the data, then load up into the public Galaxy ( usegalaxy.org) and proceed with your analysis. BEDTools works well with BED12 files. There is definitely information loss attempting to transform BED6 - BED12, as the global alignment is lost. And adjusting attributes such as score or name are often a preference, so you can alter these however you want, as long as the attribute formatting rules for the columns are followed. Hopefully this helps, Jen Galaxy team On 11/9/13 3:29 PM, lrutter @iastate.edu wrote: Hello Galaxy: I am trying overall to convert a .gff3 file to 12-column .bed file. I first tried GFF-to-BED converter, but it gave a 6-column .bed file. Then, I tried BED-to-bigBed converter by inputting the 6-column .bed file. I get an error Unspecified genome build, click the pencil icon in the history item to set the genome build. So, I click the pencil icon, and see 4 tabs at the top. I set the Attributes tab as in the attached image (Attributes.png). But then, when I select Convert Format, I am only seeing an option that outputs .bed12 file as Convert Genomic Intervals to Strict BED12. I am a bit confused about this because I specified the input file as a .bed file (and not genomic intervals, unless I am misunderstanding something). In any case, when I select Convert Genomic Intervals to Strict BED12, I do get a .bed file with 12 columns. But I would like to ask if I may have lost information going from the .gff3 to .bed(6) to .bed(12)? (I feel that scores were all set to 0 from .gff3 to .bed(6), and columns 10, 11, 12 (block counts, sizes, and starting positions) were all set to zero going from .bed(6) to .bed(12)). If I am correct that there is information loss, is there a system in Galaxy to prevent this, and transfer as much information as possible from .gff3 to .bed(12)? Thank you. L. Rutter ** Below is a head of my three files (the species is P. dominula): .gff3 file ##gff-version 3 ##date Mon Nov 4 14:54:42 2013 ##source gbrowse gbgff gff3 dumper PdomScaf0001maker gene15 1963. - . Name=PdomGene00025;ID=1;Dbxref=MAKER:maker-PdomScaf0001-snap-gene-0.274 PdomScaf0001maker mRNA15 1963. - . Name=PdomMRNA00025.1;Parent=1;ID=2;_QI=216%7C0%7C0.2%7C0.6%7C0.5%7C0.6%7C5%7C0%7C98;_eAED=0.43;_AED=0.43;Dbxref=MAKER:maker-PdomScaf0001-snap-gene-0.274-mRNA-1 PdomScaf0001maker exon15 100 -0.094 - . Parent=2;ID=3 PdomScaf0001maker CDS 15 100 . - 2 Parent=2;ID=4 PdomScaf0001maker exon223 300 21.8- . Parent=2;ID=5 PdomScaf0001maker CDS 223 300 . - 2 Parent=2;ID=6 PdomScaf0001maker exon717 765 22.4- . Parent=2;ID=7 .bed(6) file PdomScaf000114 1963gene0
Re: [galaxy-dev] launching CloudMan 2.0 on AWS
Hi Enis, Thank you for the information! I saw many GalaxyIndicesFS are accumulated on my account and cleaned up. Later I tried to launch cloudman ami, a different message I saw in paster.log: 18:35:32 - Master starting 18:35:33 - Successfully retrieved root user's public key from file. 18:35:34 - Trouble getting volume reference for volume vol-f9c4728e: EC2ResponseError: 400 Bad Request InvalidVolume.NotFoundThe volume 'vol-f9c4728e' does not exist.c69dcb4e-f924-4cbc-9c35-ef630bd18ff2 18:35:34 - Attempting to connect to a non-existent volume vol-f9c4728e 18:35:34 - Error processing filesystems in existing cluster configuration: 'NoneType' object has no attribute '__getitem__' 18:35:34 - * Manager failed to start * 18:37:14 - Initializing 'Galaxy' cluster type. Please wait... The vol-f9c4728e name I can see from the instance (ssh to the instance) is encoded in /mnt/cm/pd.yaml file. In my account I have seen the new volumes are created after launching the cloudman they are having different id's: vol-06992971 cm-3102c4d1aa831d8da4e99f3c9896390c GalaxyTools vol-05992972 cm-3102c4d1aa831d8da4e99f3c9896390c GalaxyIndices The df: Filesystem Size Used Avail Use% Mounted on /dev/xvda1 7.9G 5.2G 2.3G 70% / udev3.7G 8.0K 3.7G 1% /dev tmpfs 1.5G 228K 1.5G 1% /run none5.0M 0 5.0M 0% /run/lock none3.7G 0 3.7G 0% /run/shm cgroup 3.7G 0 3.7G 0% /sys/fs/cgroup /dev/xvdb 414G 203M 393G 1% /mnt I think I have to manually mount the new volumes to the instance then edit the configuration and restart the cludman ? or are you seeing something wrong from my side. Thanks in advance, Vipin http://galaxy.cbio.mskcc.org Hi Vipin, It seems there are too many volumes (or too much volume storage) in your AWS account and AWS is preventing any more from being created. You can either delete some volumes if you don't need them or send a request to AWS to increase your volume limit: https://aws.amazon.com/contact-us/ebs_volume_limit_request/ Cheers, Enis On Mon, Oct 14, 2013 at 10:06 PM, Vipin TS vipin...@gmail.com wrote: Hi dev-team, I am trying to launch cloudman on AWS us-east-1a and I am getting the message *All cluster services started; the cluster is ready for use. (2013-10-14 19:45:52)* I am seeing some error message in the log. * 19:05:33 - Master starting* *19:05:35 - Could not find service class matching userData service entry: PSS* *19:05:35 - Completed the initial cluster startup process. This is a new cluster; waiting to configure the type.* *19:06:11 - Migration service prerequisites OK; starting the service * *19:06:11 - SGE service prerequisites OK; starting the service* *19:06:26 - Setting up SGE...* *19:06:40 - HTCondor service prerequisites OK; starting the service* *19:06:48 - Hadoop service prerequisites OK; starting the service* *19:07:04 - Done adding Hadoop service; service running.* *19:08:13 - Initializing 'Galaxy' cluster type. Please wait...* *19:08:14 - Error creating volume: EC2ResponseError: 400 Bad Request VolumeLimitExceededMaximum number of active volumes bytes, 20, exceeded.66659429-b0dd-4f88-b763-36fd9232d3c4* *19:08:17 - Adding volume vol-f9c4728e (FS object for galaxy)...* *19:08:42 - Successfully grew file system FS object for galaxy* *19:08:42 - Successfully mounted file system /mnt/galaxy from /dev/xvdf* It seems that the galaxyIndices filesytem is not mounted to the instance. Also I am not able to start the postgres or Galaxy service through cloudman interface, both says that Cannot find the service. Please find the attached image. I think I am missing the galaxyIndices volume from the image,. any idea about the failure to launch the instance. Thanks, Vipin http://galaxy.cbio.mskcc.org ___ 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] Getting bowtie2 and tophat2 to work on galaxy on amazon aws cloud
Hi Stanislas, Please check the PATH variable and make sure that you can access bowtie2 from command line and then restart the Galaxy service through cloudman interface. I think that should work. Vipin I'm trying to run Galaxy on an Amazon AWS cloud using the normal Cloudman distribution (ami-118bfc78). The instatiated Galaxy however does not contain Bowtie2 and Tophat2, even after updating through the Cloudman Admin section. Although the wrappers are there in the tools directory, when I access it through ssh. I've also installed Bowtie2 manually on the server and the command bowtie2 does get recognized. How cat I get these two to run on the Galaxy instance? Thanks for your help. Best Stanislas ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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] Getting bowtie2 and tophat2 to work on galaxy on amazon aws cloud
- bowtie2 does not show any built-in reference genomes by default Cloudman didn't ship the genome index for bowtie2. Bowtie2 use its own index set. Usage: bowtie2-build [option] genome.fa index_basename and add the entries in bowtie2_indices.loc. Please make sure that the fields are tab delimited, not space delimited, and have no trailing or extra whitespace (this is easy to slip in by accident). and place the *.loc file under /mnt/galaxyIndices/galaxy/tool-data/ Most of the genome reference file are located at base folder: /mnt/galaxyIndices/genomes/ example: /mnt/galaxyIndices/genomes/Athaliana/araTha_tair9/seq/Arabidopsis_thaliana.TAIR9.55.dna.toplevel.fa.gz - when I try to import a file from EBI-SRA (I paste the ftp address into Upload File) it's loading without stopping until the drive is full (97 GB), although the file itself is only about 3GB. Is it a problem with the EBI server or within galaxy? I am not sure, can you please paste the url which points to the file. Thanks for any help. On Oct 14, 2013, at 5:50 PM, Vipin TS wrote: Hi Stanislas, Please check the PATH variable and make sure that you can access bowtie2 from command line and then restart the Galaxy service through cloudman interface. I think that should work. Vipin I'm trying to run Galaxy on an Amazon AWS cloud using the normal Cloudman distribution (ami-118bfc78). The instatiated Galaxy however does not contain Bowtie2 and Tophat2, even after updating through the Cloudman Admin section. Although the wrappers are there in the tools directory, when I access it through ssh. I've also installed Bowtie2 manually on the server and the command bowtie2 does get recognized. How cat I get these two to run on the Galaxy instance? Thanks for your help. Best Stanislas ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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] Deseq2 wrapper question
Yes I am agreeing on all statements. Let me finish my package and will add in one of the toolshed by today evening. I also willing to test other wrappers to improve the additional parameter settings. Tool wrappers Work In Progress from my side: DEXSeq edgeR Scripture STAR aligner SAFT multi mapper resolution This will be adding soon to the toolshed. Thanks to all, Vipin On Wed, Sep 11, 2013 at 6:08 AM, Bjoern Gruening bjoern.gruen...@gmail.comwrote: Am Mittwoch, den 11.09.2013, 10:21 +0100 schrieb Peter Cock: On Wed, Sep 11, 2013 at 10:12 AM, Joachim Jacob | VIB | joachim.ja...@vib.be wrote: It is not necessarily bad. If we all test each others tools (dependencies, interface, output,...) we might get to the best of all worlds :-) (I have planned to test Björns wrapper) One of the points of differentiation is also how 'integrated' a tool needs to be: e.g. Ross' tool for diff expression (combining a complete pipelin), and my tool just on DE with DESeq2. I like to keep things granular on the level of the tools. That is a good reason for different wrappers, one for the tool itself, and one for a larger pipeline using the same tool. And both can declare a binary package dependency via the Tool Shed using the binary dependency package Bjoern is working on, which I assume will be released on the Test Main Tool Shed under the shared IUC account once ready: http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_deseq2_1_0_17 Yes that is right, at the moment I have patches for the toolshed in preparation for a unified and easy installation of R dependencies, once that is done it will be under the IUC account. I don't see the need for 5 different wrappers. Ross approach deserves an own wrapper I think. I thought a lot about if we should use it, since it can compare 3 different approaches for DE, but it comes with some complexity. We spend some time in trying to get the UI correct and investigated some possibilities. Currently we have a few guys testing it and giving comments to our UI idea. If the ownershop is a problem, we probably can move the wrappers to a different account. But please lets merge the code base and start communicating about the UI. Thanks, Bjoern Regards, Peter ___ 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] Deseq2 wrapper question
Hello Rui, We have DESeq2 wrapper in our oqtans package and you will find this at https://github.com/ratschlab/oqtans_tools/tree/master/DESeq2 I am currently creating the associated tool_dependency.xml file for dumping the package in galaxy toolshed. otherwise it requires some manual effort to install via toolshed. May be it will help you, Vipin Hi All, we are making a wrapper for deseq2, and there is a step where control/experimental conditions need to be determined. For example, it would be a column like the following in the input file Type CTC CTC LM LM PT PT and we want the select list to contain CTC LM PT In other words, we want to filter out the 'Type' and have only distinct ones in the select list. We could make it in two steps, generate a intermediate file for this but it would be nice that we could directly retrieve the distinct types to make the list. I took a look at the tool config wiki, but didn't see anything (maybe because it was a quick scan). Does anyone have any tip on this? we'll really appreciate. Thanks, Rui ___ 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] adding new genome to local galaxy instance
H i Jen Ricardo, Thanks for the suggestions. It is resolved now. The problem was due to the tab delimiter. In my local workstation the tab was preset to four spaces. regards, Vipin Is it not showing up under the list of databases/genomes when you at these locations: 1 - Get Data - Upload File - Genome: (pull down menu) or 2 - Click on the pencil icon for any dataset, first page of 'Edit Attributes' forms Attributes - Database/Build You mentioned restarting, which is good, because that is necessary. The next thing to double check is that the names are exact and that the files are tab delimited, not space delimited, and have no trailing or extra whitespace (this is easy to slip in by accident). ___ 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] adding new genome to local galaxy instance
Hello, I am slightly confused with adding a new genome to my local Galaxy instance, I am using the recent default branch 10411:c42567f43aa7 (following the documentation at http://wiki.galaxyproject.org/Admin/Data%20Integration) I have edited the ~/galaxy-dist/tool-data/all_fasta.loc to add new Arabidopsis genome and updated ~/galaxy-dist/tool-data/shared/ucsc/builds.txt, when I restarted my local instance, I am not finding the newly added genome in database. any idea what is going wrong here ? thanks, --/Vipin ___ 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] Updating Galaxy Instance
Please follow the session Keep your code up to date at http://wiki.galaxyproject.org/Admin/Get%20Galaxy --/Vipin On Tue, Aug 27, 2013 at 10:58 AM, Richard Kuo izen...@gmail.com wrote: I can't seem to find any information on the Galaxy wiki website about the procedure for updating a local Galaxy instance to the newest release. Is there a tutorial for this somewhere? Thank you, Richard ___ 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] Public production instance page is not rendering properly
Hello dev-team,
I am experiencing a strange problem with my production instance, after I
carefully merged remote changes from galaxy-dist release to my code
repository. While restarting, It fails to load the the page properly, the
message from log file stating that serving on 0.0.0.0:8080
Here are some message found in the log file:
X.X.X.X - - [09/Aug/2013:14:30:56 -0400] GET / HTTP/1.1 500 - -
Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.34 (KHTML, like Gecko)
rekonq Safari/534.34
Error - type 'exceptions.ValueError': expected only letters, got ' en'
URL: https://galaxy.cbio.mskcc.org/
File '/codebase/lib/galaxy/web/framework/middleware/error.py', line 149 in
__call__
app_iter = self.application(environ, sr_checker)
File '/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84
in __call__
return self.application(environ, start_response)
File '/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line
633 in __call__
return self.application(environ, start_response)
File '/codebase/lib/galaxy/web/framework/base.py', line 132 in __call__
return self.handle_request( environ, start_response )
File '/codebase/lib/galaxy/web/framework/base.py', line 159 in
handle_request
trans = self.transaction_factory( environ )
File '/codebase/lib/galaxy/web/framework/__init__.py', line 238 in lambda
self.set_transaction_factory( lambda e: self.transaction_chooser( e,
galaxy_app, session_cookie ) )
File '/codebase/lib/galaxy/web/framework/__init__.py', line 269 in
transaction_chooser
return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie )
File '/codebase/lib/galaxy/web/framework/__init__.py', line 332 in __init__
self.setup_i18n()
File '/codebase/lib/galaxy/web/framework/__init__.py', line 370 in
setup_i18n
locales.append( Locale.parse( locale.split( ';' )[0], sep='-' ).language )
File '/codebase/eggs/Babel-0.9.4-py2.6.egg/babel/core.py', line 212 in parse
return cls(*parse_locale(identifier, sep=sep))
File '/codebase/eggs/Babel-0.9.4-py2.6.egg/babel/core.py', line 763 in
parse_locale
raise ValueError('expected only letters, got %r' % lang)
ValueError: expected only letters, got ' en'
CGI Variables
-
CONTENT_LENGTH: '0'
HTTP_ACCEPT:
'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
HTTP_ACCEPT_CHARSET: 'utf-8,*;q=0.5'
HTTP_ACCEPT_ENCODING: 'gzip, deflate, x-gzip, x-deflate'
HTTP_ACCEPT_LANGUAGE: 'en-US, en-US; q=0.8, en; q=0.6'
HTTP_CACHE_CONTROL: 'max-age=0'
HTTP_CONNECTION: 'Keep-Alive'
HTTP_HOST: 'galaxy.cbio.mskcc.org'
HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.34
(KHTML, like Gecko) rekonq Safari/534.34'
HTTP_X_FORWARDED_FOR: '172.21.50.129'
HTTP_X_FORWARDED_HOST: 'galaxy.cbio.mskcc.org'
HTTP_X_FORWARDED_SERVER: 'galaxy.cbio.mskcc.org'
HTTP_X_URL_SCHEME: 'https'
ORGINAL_HTTP_HOST: 'localhost:8081'
ORGINAL_REMOTE_ADDR: '127.0.0.1'
PATH_INFO: '/'
REMOTE_ADDR: '172.21.50.129'
REQUEST_METHOD: 'GET'
SERVER_NAME: '0.0.0.0'
SERVER_PORT: '8081'
SERVER_PROTOCOL: 'HTTP/1.1'
WSGI Variables
--
application: paste.recursive.RecursiveMiddleware object at 0x7f78910
is_api_request: False
original_wsgi.url_scheme: 'http'
paste.expected_exceptions: [class 'paste.httpexceptions.HTTPException']
paste.httpexceptions: paste.httpexceptions.HTTPExceptionHandler object
at 0x7f78210
paste.httpserver.thread_pool: paste.httpserver.ThreadPool object at
0x8066d90
paste.recursive.forward: paste.recursive.Forwarder from /
paste.recursive.include: paste.recursive.Includer from /
paste.recursive.include_app_iter: paste.recursive.IncluderAppIter from /
paste.recursive.script_name: ''
paste.throw_errors: True
request_id: 'd4f643a8012111e3819090b11c087d99'
wsgi process: 'Multithreaded'
Any idea what is going wrong here? Please let me know if you need more get
more details.
Many thanks,
--/Vipin
___
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:
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To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] Public production instance page is not rendering properly
for using Galaxy,
Dan
On Aug 9, 2013, at 2:33 PM, Vipin TS wrote:
Hello dev-team,
I am experiencing a strange problem with my production instance, after I
carefully merged remote changes from galaxy-dist release to my code
repository. While restarting, It fails to load the the page properly, the
message from log file stating that serving on 0.0.0.0:8080
Here are some message found in the log file:
X.X.X.X - - [09/Aug/2013:14:30:56 -0400] GET / HTTP/1.1 500 - -
Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.34 (KHTML, like Gecko)
rekonq Safari/534.34
Error - type 'exceptions.ValueError': expected only letters, got ' en'
URL: https://galaxy.cbio.mskcc.org/
File '/codebase/lib/galaxy/web/framework/middleware/error.py', line 149 in
__call__
app_iter = self.application(environ, sr_checker)
File '/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84
in __call__
return self.application(environ, start_response)
File '/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py',
line 633 in __call__
return self.application(environ, start_response)
File '/codebase/lib/galaxy/web/framework/base.py', line 132 in __call__
return self.handle_request( environ, start_response )
File '/codebase/lib/galaxy/web/framework/base.py', line 159 in
handle_request
trans = self.transaction_factory( environ )
File '/codebase/lib/galaxy/web/framework/__init__.py', line 238 in lambda
self.set_transaction_factory( lambda e: self.transaction_chooser( e,
galaxy_app, session_cookie ) )
File '/codebase/lib/galaxy/web/framework/__init__.py', line 269 in
transaction_chooser
return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie )
File '/codebase/lib/galaxy/web/framework/__init__.py', line 332 in __init__
self.setup_i18n()
File '/codebase/lib/galaxy/web/framework/__init__.py', line 370 in
setup_i18n
locales.append( Locale.parse( locale.split( ';' )[0], sep='-' ).language
)
File '/codebase/eggs/Babel-0.9.4-py2.6.egg/babel/core.py', line 212 in
parse
return cls(*parse_locale(identifier, sep=sep))
File '/codebase/eggs/Babel-0.9.4-py2.6.egg/babel/core.py', line 763 in
parse_locale
raise ValueError('expected only letters, got %r' % lang)
ValueError: expected only letters, got ' en'
CGI Variables
-
CONTENT_LENGTH: '0'
HTTP_ACCEPT:
'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
HTTP_ACCEPT_CHARSET: 'utf-8,*;q=0.5'
HTTP_ACCEPT_ENCODING: 'gzip, deflate, x-gzip, x-deflate'
HTTP_ACCEPT_LANGUAGE: 'en-US, en-US; q=0.8, en; q=0.6'
HTTP_CACHE_CONTROL: 'max-age=0'
HTTP_CONNECTION: 'Keep-Alive'
HTTP_HOST: 'galaxy.cbio.mskcc.org'
HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.34
(KHTML, like Gecko) rekonq Safari/534.34'
HTTP_X_FORWARDED_FOR: '172.21.50.129'
HTTP_X_FORWARDED_HOST: 'galaxy.cbio.mskcc.org'
HTTP_X_FORWARDED_SERVER: 'galaxy.cbio.mskcc.org'
HTTP_X_URL_SCHEME: 'https'
ORGINAL_HTTP_HOST: 'localhost:8081'
ORGINAL_REMOTE_ADDR: '127.0.0.1'
PATH_INFO: '/'
REMOTE_ADDR: '172.21.50.129'
REQUEST_METHOD: 'GET'
SERVER_NAME: '0.0.0.0'
SERVER_PORT: '8081'
SERVER_PROTOCOL: 'HTTP/1.1'
WSGI Variables
--
application: paste.recursive.RecursiveMiddleware object at 0x7f78910
is_api_request: False
original_wsgi.url_scheme: 'http'
paste.expected_exceptions: [class 'paste.httpexceptions.HTTPException']
paste.httpexceptions: paste.httpexceptions.HTTPExceptionHandler object
at 0x7f78210
paste.httpserver.thread_pool: paste.httpserver.ThreadPool object at
0x8066d90
paste.recursive.forward: paste.recursive.Forwarder from /
paste.recursive.include: paste.recursive.Includer from /
paste.recursive.include_app_iter: paste.recursive.IncluderAppIter from
/
paste.recursive.script_name: ''
paste.throw_errors: True
request_id: 'd4f643a8012111e3819090b11c087d99'
wsgi process: 'Multithreaded'
Any idea what is going wrong here? Please let me know if you need more get
more details.
Many thanks,
--/Vipin
___
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] Public production instance page is not rendering properly
Hi Dan,
I deleted the
contents from
/codebase/database/complied_templates/* and restarted the instance, still
no luck. Sorry.
Thanks, Vipin
On Fri, Aug 9, 2013 at 3:43 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Vipin,
Can you try deleting the contents of your compiled templates directory
(i.e.
/codebase/database/compiled_templates/*)?
Thanks for using Galaxy,
Dan
On Aug 9, 2013, at 3:22 PM, Vipin TS wrote:
Hi Dan,
Thanks for the information, I have updated this to my repository manually.
Now I can invoke the page but the frames were not loaded correctly.
The log message as follows:
/codebase/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/sql/expression.py:1927:
SAWarning: The IN-predicate on request_type.id was invoked with an
empty sequence. This results in a contradiction, which nonetheless can be
expensive to evaluate. Consider alternative strategies for improved
performance.
X.X.X.X - - [09/Aug/2013:15:09:55 -0400] GET / HTTP/1.1 200 - -
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.26.17
(KHTML, like Gecko) Version/6.0.2 Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /root/tool_menu HTTP/1.1
404 - https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel Mac
OS X 10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /history HTTP/1.1 200 -
https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel Mac OS X
10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /history HTTP/1.1 500 -
https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel Mac OS X
10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
Exception happened during processing of request from ('127.0.0.1', 43370)
Traceback (most recent call last):
File /codebase/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 617, in __init__
self.handle()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
442, in handle
BaseHTTPRequestHandler.handle(self)
File /usr/lib64/python2.6/BaseHTTPServer.py, line 329, in handle
self.handle_one_request()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
437, in handle_one_request
self.wsgi_execute()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
287, in wsgi_execute
self.wsgi_start_response)
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/urlmap.py, line 203,
in __call__
return app(environ, start_response)
File /codebase/lib/galaxy/web/framework/middleware/request_id.py, line
12, in __call__
return self.app( environ, start_response )
File /codebase/lib/galaxy/web/framework/middleware/xforwardedhost.py,
line 21, in __call__
return self.app( environ, start_response )
File /codebase/lib/galaxy/web/framework/middleware/translogger.py,
line 68, in __call__
return self.application(environ, replacement_start_response)
File /codebase/lib/galaxy/web/framework/middleware/error.py, line 159,
in __call__
exc_info)
File /codebase/lib/galaxy/web/framework/middleware/translogger.py,
line 67, in replacement_start_response
return start_response( status, headers, exc_info )
File /codebase/lib/galaxy/web/framework/middleware/error.py, line 149,
in __call__
app_iter = self.application(environ, sr_checker)
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py, line
84, in __call__
return self.application(environ, start_response)
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py,
line 633, in __call__
return self.application(environ, start_response)
File /codebase/lib/galaxy/web/framework/base.py, line 132, in __call__
return self.handle_request( environ, start_response )
File /codebase/lib/galaxy/web/framework/base.py, line 199, in
handle_request
return body( environ, start_response )
File /codebase/lib/galaxy/web/framework/__init__.py, line 985, in
render
template.render_context( context )
File /codebase/eggs/Mako-0.4.1-py2.6.egg/mako/template.py, line 319,
in render_context
**kwargs)
File /codebase/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py, line 692, in
_render_context
_exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
File /codebase/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py, line 718, in
_exec_template
callable_(context, *args, **kwargs)
File /codebase/database/compiled_templates/root/history.mako.py, line
73, in render_body
if bool( [ data for data
[galaxy-dev] Fwd: Public production instance page is not rendering properly
--/Vipin
-- Forwarded message --
From: Vipin TS vipin...@gmail.com
Date: Fri, Aug 9, 2013 at 5:04 PM
Subject: Re: [galaxy-dev] Public production instance page is not rendering
properly
To: Daniel Blankenberg d...@bx.psu.edu
Hi Dan,
Thanks for your support, Hmm, I can see that there are changes:
but here is the out come from the below commands:
$$
hg diff templates/webapps/galaxy/root/history.mako
empty
$$
hg summary
parent: 10218:ff0bd4a811d9 tip
merged the changes from stable release version July 2013 from bx.psu.edu
branch: default
commit: 5 modified, 5 removed, 452 deleted
update: 1663 new changesets, 2 branch heads (merge)
$$hg config
Sorry, it says unknown option.
Do you think I have mixed up something ?
Thank you, Vipin
On Fri, Aug 9, 2013 at 4:41 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Vipin,
Strange, are you running the latest galaxy-dist? That line doesn't exist
in e.g.
https://bitbucket.org/galaxy/galaxy-dist/src/ebe87051fadff5750ec226490b31e49bdd68b070/templates/webapps/galaxy/root/history.mako?at=default.
Can you compare your file to the file in the repository? What is the output
of:
hg diff templates/webapps/galaxy/root/history.mako
and
hg summary
and
hg config
Thanks for using Galaxy,
Dan
On Aug 9, 2013, at 3:56 PM, Vipin TS wrote:
Hi Dan,
I deleted the
contents from
/codebase/database/complied_templates/* and restarted the instance, still
no luck. Sorry.
Thanks, Vipin
On Fri, Aug 9, 2013 at 3:43 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Vipin,
Can you try deleting the contents of your compiled templates directory
(i.e.
/codebase/database/compiled_templates/*)?
Thanks for using Galaxy,
Dan
On Aug 9, 2013, at 3:22 PM, Vipin TS wrote:
Hi Dan,
Thanks for the information, I have updated this to my repository
manually. Now I can invoke the page but the frames were not loaded
correctly.
The log message as follows:
/codebase/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/sql/expression.py:1927:
SAWarning: The IN-predicate on request_type.id was invoked with an
empty sequence. This results in a contradiction, which nonetheless can be
expensive to evaluate. Consider alternative strategies for improved
performance.
X.X.X.X - - [09/Aug/2013:15:09:55 -0400] GET / HTTP/1.1 200 - -
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.26.17
(KHTML, like Gecko) Version/6.0.2 Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /root/tool_menu HTTP/1.1
404 - https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel
Mac OS X 10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /history HTTP/1.1 200 -
https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel Mac OS X
10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /history HTTP/1.1 500 -
https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel Mac OS X
10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
Exception happened during processing of request from ('127.0.0.1', 43370)
Traceback (most recent call last):
File /codebase/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 617, in __init__
self.handle()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
442, in handle
BaseHTTPRequestHandler.handle(self)
File /usr/lib64/python2.6/BaseHTTPServer.py, line 329, in handle
self.handle_one_request()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
437, in handle_one_request
self.wsgi_execute()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
287, in wsgi_execute
self.wsgi_start_response)
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/urlmap.py, line
203, in __call__
return app(environ, start_response)
File /codebase/lib/galaxy/web/framework/middleware/request_id.py,
line 12, in __call__
return self.app( environ, start_response )
File /codebase/lib/galaxy/web/framework/middleware/xforwardedhost.py,
line 21, in __call__
return self.app( environ, start_response )
File /codebase/lib/galaxy/web/framework/middleware/translogger.py,
line 68, in __call__
return self.application(environ, replacement_start_response)
File /codebase/lib/galaxy/web/framework/middleware/error.py, line
159, in __call__
exc_info)
File /codebase/lib/galaxy/web/framework/middleware/translogger.py,
line 67, in replacement_start_response
return start_response( status, headers
Re: [galaxy-dev] Public production instance page is not rendering properly
Hi Dan,
hg config for our repository is:
cat .hg/hgrc
[paths]
default = http://www.bx.psu.edu/hg/galaxy
[ui]
username = Galaxy RaetschLab gal...@raetschlab.org
verbose = True
merge = vimdiff
[merge-tools]
vimdiff.executable = vim
vimdiff.args = -d $base $local $output $other +close +close
Thanks, Vipin
Hi Dan,
Thanks for your support, Hmm, I can see that there are changes:
but here is the out come from the below commands:
$$
hg diff templates/webapps/galaxy/root/history.mako
empty
$$
hg summary
parent: 10218:ff0bd4a811d9 tip
merged the changes from stable release version July 2013 from bx.psu.edu
branch: default
commit: 5 modified, 5 removed, 452 deleted
update: 1663 new changesets, 2 branch heads (merge)
$$hg config
Sorry, it says unknown option.
Do you think I have mixed up something ?
Thank you, Vipin
On Fri, Aug 9, 2013 at 4:41 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Vipin,
Strange, are you running the latest galaxy-dist? That line doesn't exist
in e.g.
https://bitbucket.org/galaxy/galaxy-dist/src/ebe87051fadff5750ec226490b31e49bdd68b070/templates/webapps/galaxy/root/history.mako?at=default.
Can you compare your file to the file in the repository? What is the output
of:
hg diff templates/webapps/galaxy/root/history.mako
and
hg summary
and
hg config
Thanks for using Galaxy,
Dan
On Aug 9, 2013, at 3:56 PM, Vipin TS wrote:
Hi Dan,
I deleted the
contents from
/codebase/database/complied_templates/* and restarted the instance,
still no luck. Sorry.
Thanks, Vipin
On Fri, Aug 9, 2013 at 3:43 PM, Daniel Blankenberg d...@bx.psu.eduwrote:
Hi Vipin,
Can you try deleting the contents of your compiled templates directory
(i.e.
/codebase/database/compiled_templates/*)?
Thanks for using Galaxy,
Dan
On Aug 9, 2013, at 3:22 PM, Vipin TS wrote:
Hi Dan,
Thanks for the information, I have updated this to my repository
manually. Now I can invoke the page but the frames were not loaded
correctly.
The log message as follows:
/codebase/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/sql/expression.py:1927:
SAWarning: The IN-predicate on request_type.id was invoked with an
empty sequence. This results in a contradiction, which nonetheless can be
expensive to evaluate. Consider alternative strategies for improved
performance.
X.X.X.X - - [09/Aug/2013:15:09:55 -0400] GET / HTTP/1.1 200 - -
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.26.17
(KHTML, like Gecko) Version/6.0.2 Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /root/tool_menu HTTP/1.1
404 - https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel
Mac OS X 10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /history HTTP/1.1 200 -
https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel Mac OS X
10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
X.X.X.X - - [09/Aug/2013:15:09:56 -0400] GET /history HTTP/1.1 500 -
https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (Macintosh; Intel Mac OS X
10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
Exception happened during processing of request from ('127.0.0.1', 43370)
Traceback (most recent call last):
File /codebase/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 617, in __init__
self.handle()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py,
line 442, in handle
BaseHTTPRequestHandler.handle(self)
File /usr/lib64/python2.6/BaseHTTPServer.py, line 329, in handle
self.handle_one_request()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py,
line 437, in handle_one_request
self.wsgi_execute()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py,
line 287, in wsgi_execute
self.wsgi_start_response)
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/urlmap.py, line
203, in __call__
return app(environ, start_response)
File /codebase/lib/galaxy/web/framework/middleware/request_id.py,
line 12, in __call__
return self.app( environ, start_response )
File
/codebase/lib/galaxy/web/framework/middleware/xforwardedhost.py, line 21,
in __call__
return self.app( environ, start_response )
File /codebase/lib/galaxy/web/framework/middleware/translogger.py,
line 68, in __call__
return self.application(environ, replacement_start_response)
File /codebase/lib/galaxy/web/framework/middleware/error.py, line
159, in __call__
exc_info)
File /codebase/lib/galaxy/web/framework/middleware/translogger.py
[galaxy-dev] (no subject)
Hello dev-team,
I have updated
code repository
of our production instance https://galaxy.cbio.mskcc.org to the recent
galaxy-dist (10216:ebe87051fadf), now the instance page it is not rendering
in a proper way.
The error message I can see from the log file as follows:
--
x.x.x.x - - [08/Aug/2013:15:00:49 -0400] GET / HTTP/1.1 200 - -
Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.31 (KHTML, like Gecko)
Chrome/26.0.1410.63 Safari/537.31
x.x.x.x - - [08/Aug/2013:15:00:50 -0400] GET /root/tool_menu HTTP/1.1 404
- https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (X11; Linux x86_64)
AppleWebKit/537.31 (KHTML, like Gecko) Chrome/26.0.1410.63 Safari/537.31
x.x.x.x - - [08/Aug/2013:15:00:50 -0400] GET /history HTTP/1.1 200 -
https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (X11; Linux x86_64)
AppleWebKit/537.31 (KHTML, like Gecko) Chrome/26.0.1410.63 Safari/537.31
x.x.x.x - - [08/Aug/2013:15:00:50 -0400] GET /history HTTP/1.1 500 -
https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (X11; Linux x86_64)
AppleWebKit/537.31 (KHTML, like Gecko) Chrome/26.0.1410.63 Safari/537.31
Exception happened during processing of request from ('127.0.0.1', 42042)
Traceback (most recent call last):
File /codebase/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 617, in __init__
self.handle()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
442, in handle
BaseHTTPRequestHandler.handle(self)
File /usr/lib64/python2.6/BaseHTTPServer.py, line 329, in handle
self.handle_one_request()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
437, in handle_one_request
self.wsgi_execute()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
287, in wsgi_execute
self.wsgi_start_response)
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/urlmap.py, line 203,
in __call__
return app(environ, start_response)
File /codebase/lib/galaxy/web/framework/middleware/request_id.py, line
12, in __call__
return self.app( environ, start_response )
File /codebase/lib/galaxy/web/framework/middleware/xforwardedhost.py,
line 21, in __call__
return self.app( environ, start_response )
File /codebase/lib/galaxy/web/framework/middleware/translogger.py, line
68, in __call__
return self.application(environ, replacement_start_response)
File /codebase/lib/galaxy/web/framework/middleware/error.py, line 159,
in __call__
exc_info)
File /codebase/lib/galaxy/web/framework/middleware/translogger.py, line
67, in replacement_start_response
return start_response( status, headers, exc_info )
File /codebase/lib/galaxy/web/framework/middleware/error.py, line 149,
in __call__
app_iter = self.application(environ, sr_checker)
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py, line
84, in __call__
return self.application(environ, start_response)
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py,
line 633, in __call__
return self.application(environ, start_response)
File /codebase/lib/galaxy/web/framework/base.py, line 132, in __call__
return self.handle_request( environ, start_response )
File /codebase/lib/galaxy/web/framework/base.py, line 199, in
handle_request
return body( environ, start_response )
File /codebase/lib/galaxy/web/framework/__init__.py, line 985, in render
template.render_context( context )
File /codebase/eggs/Mako-0.4.1-py2.6.egg/mako/template.py, line 319, in
render_context
**kwargs)
File /codebase/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py, line 692, in
_render_context
_exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
File /codebase/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py, line 718, in
_exec_template
callable_(context, *args, **kwargs)
File /codebase/database/compiled_templates/root/history.mako.py, line
73, in render_body
if bool( [ data for data in history.active_datasets if data.state in
['running', 'queued', '', None ] ] ):
AttributeError: 'Undefined' object has no attribute 'active_datasets'
Could you point me where I have to look to fix this issue.
thanks in advance,
--/Vipin
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[galaxy-dev] instance restart fails with AttributeError: 'module' object has no attribute 'DataManagerHistoryAssociation'
Hello dev-team, I am trying to upgrade our production instance to the latest release (to galaxy-dist) , somehow I am not able to restart the instance. Here is the log message I found: File ./scripts/paster.py, line 35, in module serve.run() File galaxy-prod-repo/lib/galaxy/util/pastescript/serve.py, line 1049, in run invoke(command, command_name, options, args[1:]) File galaxy-prod-repo/lib/galaxy/util/pastescript/serve.py, line 1055, in invoke exit_code = runner.run(args) File galaxy-prod-repo/lib/galaxy/util/pastescript/serve.py, line 220, in run result = self.command() File galaxy-prod-repo/lib/galaxy/util/pastescript/serve.py, line 643, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File galaxy-prod-repo/lib/galaxy/util/pastescript/loadwsgi.py, line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File galaxy-prod-repo/lib/galaxy/util/pastescript/loadwsgi.py, line 374, in loadobj global_conf=global_conf) File galaxy-prod-repo/lib/galaxy/util/pastescript/loadwsgi.py, line 399, in loadcontext global_conf=global_conf) File galaxy-prod-repo/lib/galaxy/util/pastescript/loadwsgi.py, line 423, in _loadconfig return loader.get_context(object_type, name, global_conf) File galaxy-prod-repo/lib/galaxy/util/pastescript/loadwsgi.py, line 561, in get_context section) File galaxy-prod-repo/lib/galaxy/util/pastescript/loadwsgi.py, line 620, in _context_from_explicit value = import_string(found_expr) File galaxy-prod-repo/lib/galaxy/util/pastescript/loadwsgi.py, line 125, in import_string return pkg_resources.EntryPoint.parse(x= + s).load(False) File galaxy-prod-repo/lib/pkg_resources.py, line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File galaxy-prod-repo/lib/galaxy/web/buildapp.py, line 3, in module from galaxy.webapps.galaxy.buildapp import app_factory File galaxy-prod-repo/lib/galaxy/webapps/galaxy/buildapp.py, line 18, in module import galaxy.model.mapping File galaxy-prod-repo/lib/galaxy/model/mapping.py, line 943, in module Column( user_id, Integer, ForeignKey( galaxy_user.id ), index=True ) AttributeError: 'module' object has no attribute 'DataManagerHistoryAssociation' Removing PID file paster.pid I am not clear about the error message here. any idea thank you, --/Vipin cBio MSKCC Ratsch Lab ___ 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] moving galaxy published pages
Hello dev-team, Usually when I want to move a Galaxy Published Page between instances I follows these steps: (a) moving workflows and dataset from instance_1 to instance_2 (b) run the workflow at instance_2 (c) create the page at instance_2 So my question is - Can I move/share published pages between instances other than the above way just curious to know, --/Vipin ___ 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] galaxysession cookie secure flag
Hello, I figured out the place where the cookie gets set in Galaxy and then add secure to that. Apache configuration didn't work well. added the following code into function set_cookie in: lib/galaxy/web/framework/__init__.py *def set_cookie( self, value, name='galaxysession', path='/', age=90, version='1' ): * * try: * * self.response.cookies[name]['secure'] = True * * except CookieError, e: * * log.warning( Error setting secure attribute in cookie '%s': %s % ( name, e ) )* I tested by running the following, now I can see the flag secure in the set-cookie curl -k -D - https://gx.cbio.mskcc.org/ -o /dev/null % Total% Received % Xferd Average Speed TimeTime Time Current Dload Upload Total SpentLeft Speed 0 00 00 0 0 0 --:--:-- --:--:-- --:--:-- 0HTTP/1.1 200 OK Date: Mon, 06 May 2013 14:50:16 GMT Server: PasteWSGIServer/0.5 Python/2.6.6 content-type: text/html; charset=UTF-8 Set-Cookie: galaxysession=7cf35ade3e68eef6c0bd6866318609b987df86a0d50ecc280f02efaa5966a9aa59ce7177812bed97; expires=Sun, 04-Aug-2013 10:50:16 GMT; httponly; Max-Age=7776000; Path=/; secure; Version=1 Connection: close Transfer-Encoding: chunked 100 253950 253950 0 35881 0 --:--:-- --:--:-- --:--:-- 69575 --Vipin Hi dev-team, We have placed our galaxy instance ssl and I need to make sure that the secure flag is set on the cookie (commonly represented by the word “secure” under the Security column) but I am not able to do the same. something like below: [image: Inline image 2] when I checked on my instance I saw as below: [image: Inline image 3] I have made necessary changes to my ssl.conf to put the flag as secure, but it seems not appearing here. Header edit Set-Cookie ^(.*)$ $1;Secure;HttpOnly does anybody have an experience in setting up the same. thanks in advance, --/Vipin image.pngimage.png___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] user password different type encoding
Thanks James!
I have pulled the recent changes to my repository and this is working fine.
I have tested with creating a new user
and I tried to login with the recently created user and this works fine at
my end. The entry looks like as follows:
galaxy=# select username,email,password from galaxy_user where email = '
c...@gmail.com';
username | email | password
--++---
cbio | c...@gmail.com |
PBKDF2$sha256$1$7CWpfEOjZ3xmRH6b$ufFHb8Ax9GkVBGmnR5fq159NA3C4F6o0
This works fine.
With this new implementation, the new registration password hashes are
generated in PBKDF2. May be one can force
the existing users to reset the password, so that all users password will
be updated in the table. As you mentioned in the
previous mail, because of random salt generation in the password hashing
step, I don't think I can take all of the existing
user’s SHA-1 hashes, run them through the algorithm and replace them with
the updated hashes. I thought this would
be transparent to the users instead of forcing to reset the password.
any thoughts on this?
Thank you for timely help,
--Vipin
Rather than committing this directly I created the following pull request:
https://bitbucket.org/galaxy/galaxy-central/pull-request/165/password-security-use-pbkdf2-scheme-with
It would be great if a couple of people could sign-off on it before
merging. I don't think I'm doing anything stupid, but a sanity check
is appreciated.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Sun, May 5, 2013 at 12:12 PM, James Taylor ja...@jamestaylor.org
wrote:
Vipin, I think the main problem here is that you cannot treat PBKDF2
as a hash in this way. Every time you hash the same password you get a
different result because you are generating a new random salt.
Instead, you need to decode the in database representation to extract
the salt and then do a comparison on the hashed part.
I have this working in a backward compatible way, and I think it is a
good idea so I will be committing it to central shortly.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Thu, May 2, 2013 at 2:34 PM, Vipin TS vipin...@gmail.com wrote:
Thanks James, I have updated the password of one user in galaxy_user
table
with the new algorithm,
I also adjusted the function new_secure_hash in
/lib/galaxy/util/hash_util.py in such a way that it returns
the new hash instead of sha1. Now I tried to login, it fails to get the
account, I think there is something going
wrong in the password hash comparison. Can you please assit here.
+++ b/lib/galaxy/util/hash_util.py Thu May 02 14:33:07 2013 -0400
@@ -25,13 +25,60 @@
Returns either a sha1 hash object (if called with no arguments),
or a
hexdigest of the sha1 hash of the argument `text_type`.
+import hashlib
+from os import urandom
+from base64 import b64encode, b64decode
+from itertools import izip
+from pbkdf2 import pbkdf2_bin
+
+SALT_LENGTH = 12
+KEY_LENGTH = 24
+HASH_FUNCTION = 'sha256'
+COST_FACTOR = 1
+
if text_type:
+#return sha1( text_type ).hexdigest()
+
+sec_hash_1 = sha1( text_type ).hexdigest()
+
+if isinstance(sec_hash_1, unicode):
+sec_hash_1 = sec_hash_1.encode('utf-8')
+salt = b64encode(urandom(SALT_LENGTH))
+
+return 'PBKDF2${0}${1}${2}${3}'.format(
+HASH_FUNCTION,
+COST_FACTOR,
+salt,
+b64encode(pbkdf2_bin(sec_hash_1, salt, COST_FACTOR,
KEY_LENGTH,
getattr(hashlib, HASH_FUNCTION
thanks, Vipin
That should be the only place, it is called from the some methods of
the User model object. So you could modify it to always hash new
passwords in a different way, but check old passwords with sha1 first,
then something else.
Although it might be nice to move the functionality into
security.validate_user_input since it is really specific to user
passwords, especially with those changes.
I'd be happy to see this go into main with sha256 or something
similar. Also, we could consider adding a random per-user salt field
if you are really concerned about this.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Thu, May 2, 2013 at 10:21 AM, Vipin TS vipin...@gmail.com wrote:
Hello dev-team,
I would like to add the different type of password encryption to the
users
in my galaxy instance. I started working with the current password
encoding
script:
/home/apps/galaxy-dist/lib/galaxy/util/hash_util.py
I will keep the current sha1 and add another layer of encryption to
the
sha1
hash, otherwise I need to force all my users to change the password
and
follow the new hashing
[galaxy-dev] user password different type encoding
Hello dev-team, I would like to add the different type of password encryption to the users in my galaxy instance. I started working with the current password encoding script: /home/apps/galaxy-dist/lib/galaxy/util/hash_util.py I will keep the current sha1 and add another layer of encryption to the sha1 hash, otherwise I need to force all my users to change the password and follow the new hashing method. Can anyone please point me any other place/script which I missed regarding the encryption/decryption of user authentication. thanks in advance, --/Vipin ___ 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] user password different type encoding
Thanks James, I have updated the password of one user in galaxy_user table
with the new algorithm,
I also adjusted the function new_secure_hash
in /lib/galaxy/util/hash_util.py in such a way that it returns
the new hash instead of sha1. Now I tried to login, it fails to get the
account, I think there is something going
wrong in the password hash comparison. Can you please assit here.
+++ b/lib/galaxy/util/hash_util.py Thu May 02 14:33:07 2013 -0400
@@ -25,13 +25,60 @@
Returns either a sha1 hash object (if called with no arguments), or a
hexdigest of the sha1 hash of the argument `text_type`.
+import hashlib
+from os import urandom
+from base64 import b64encode, b64decode
+from itertools import izip
+from pbkdf2 import pbkdf2_bin
+
+SALT_LENGTH = 12
+KEY_LENGTH = 24
+HASH_FUNCTION = 'sha256'
+COST_FACTOR = 1
+
if text_type:
+#return sha1( text_type ).hexdigest()
+
+sec_hash_1 = sha1( text_type ).hexdigest()
+
+if isinstance(sec_hash_1, unicode):
+sec_hash_1 = sec_hash_1.encode('utf-8')
+salt = b64encode(urandom(SALT_LENGTH))
+
+return 'PBKDF2${0}${1}${2}${3}'.format(
+HASH_FUNCTION,
+COST_FACTOR,
+salt,
+b64encode(pbkdf2_bin(sec_hash_1, salt, COST_FACTOR,
KEY_LENGTH, getattr(hashlib, HASH_FUNCTION
thanks, Vipin
That should be the only place, it is called from the some methods of
the User model object. So you could modify it to always hash new
passwords in a different way, but check old passwords with sha1 first,
then something else.
Although it might be nice to move the functionality into
security.validate_user_input since it is really specific to user
passwords, especially with those changes.
I'd be happy to see this go into main with sha256 or something
similar. Also, we could consider adding a random per-user salt field
if you are really concerned about this.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Thu, May 2, 2013 at 10:21 AM, Vipin TS vipin...@gmail.com wrote:
Hello dev-team,
I would like to add the different type of password encryption to the
users
in my galaxy instance. I started working with the current password
encoding
script:
/home/apps/galaxy-dist/lib/galaxy/util/hash_util.py
I will keep the current sha1 and add another layer of encryption to the
sha1
hash, otherwise I need to force all my users to change the password and
follow the new hashing method.
Can anyone please point me any other place/script which I missed
regarding
the encryption/decryption of user authentication.
thanks in advance,
--/Vipin
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[galaxy-dev] galaxysession cookie secure flag
Hi dev-team, We have placed our galaxy instance ssl and I need to make sure that the secure flag is set on the cookie (commonly represented by the word “secure” under the Security column) but I am not able to do the same. something like below: [image: Inline image 2] when I checked on my instance I saw as below: [image: Inline image 3] I have made necessary changes to my ssl.conf to put the flag as secure, but it seems not appearing here. Header edit Set-Cookie ^(.*)$ $1;Secure;HttpOnly does anybody have an experience in setting up the same. thanks in advance, --/Vipin image.pngimage.png___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] user password different type encoding
I have started testing with creating a new user and the password hash
created using new algorithm,
galaxy=# select username,email,password from galaxy_user where email = '
fml...@gmail.com';
username | email | password
--+--+--
| fml...@gmail.com | PBKDF2$sha256$1$e0DVCuGEua3ebxxU$Bh6
I have updated the length of password column to 80 characters in my table
and still the stored password
seems to be in 40 char long, I print the hash after creating the second
hash (password - sha1 hash 40 char long- pbdkf2 hash 69 char long)
before storing into the database table, I believing the hash has
been truncated, any idea what is happening here.
I am not seeing any clue in the code.
thanks, Vipin
Thanks James, I have updated the password of one user in galaxy_user table
with the new algorithm,
I also adjusted the function new_secure_hash
in /lib/galaxy/util/hash_util.py in such a way that it returns
the new hash instead of sha1. Now I tried to login, it fails to get the
account, I think there is something going
wrong in the password hash comparison. Can you please assit here.
+++ b/lib/galaxy/util/hash_util.py Thu May 02 14:33:07 2013 -0400
@@ -25,13 +25,60 @@
Returns either a sha1 hash object (if called with no arguments), or a
hexdigest of the sha1 hash of the argument `text_type`.
+import hashlib
+from os import urandom
+from base64 import b64encode, b64decode
+from itertools import izip
+from pbkdf2 import pbkdf2_bin
+
+SALT_LENGTH = 12
+KEY_LENGTH = 24
+HASH_FUNCTION = 'sha256'
+COST_FACTOR = 1
+
if text_type:
+#return sha1( text_type ).hexdigest()
+
+sec_hash_1 = sha1( text_type ).hexdigest()
+
+if isinstance(sec_hash_1, unicode):
+sec_hash_1 = sec_hash_1.encode('utf-8')
+salt = b64encode(urandom(SALT_LENGTH))
+
+return 'PBKDF2${0}${1}${2}${3}'.format(
+HASH_FUNCTION,
+COST_FACTOR,
+salt,
+b64encode(pbkdf2_bin(sec_hash_1, salt, COST_FACTOR,
KEY_LENGTH, getattr(hashlib, HASH_FUNCTION
thanks, Vipin
That should be the only place, it is called from the some methods of
the User model object. So you could modify it to always hash new
passwords in a different way, but check old passwords with sha1 first,
then something else.
Although it might be nice to move the functionality into
security.validate_user_input since it is really specific to user
passwords, especially with those changes.
I'd be happy to see this go into main with sha256 or something
similar. Also, we could consider adding a random per-user salt field
if you are really concerned about this.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Thu, May 2, 2013 at 10:21 AM, Vipin TS vipin...@gmail.com wrote:
Hello dev-team,
I would like to add the different type of password encryption to the
users
in my galaxy instance. I started working with the current password
encoding
script:
/home/apps/galaxy-dist/lib/galaxy/util/hash_util.py
I will keep the current sha1 and add another layer of encryption to the
sha1
hash, otherwise I need to force all my users to change the password and
follow the new hashing method.
Can anyone please point me any other place/script which I missed
regarding
the encryption/decryption of user authentication.
thanks in advance,
--/Vipin
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Re: [galaxy-dev] user password different type encoding
I have updated the table schema from the script to adjust the column length
from the following script:
lib/galaxy/model/mapping.py
Now my new registration passwords are encrypted with second layer of
authentication using PBKDF2
new entry from the database table:
galaxy=# select username,email,password from galaxy_user where email = '
vi...@mail.com';
username | email | password
--++---
| vi...@mail.com |
PBKDF2$sha256$1$lv0RfxbU3SymKvEA$l4RH9f9xHrH4pcf9n6ELP1MWjG+hooEW
BUT now I am experiencing the problem with authenticating the newly
registered user name. once I log out,
I can’t log back in again – password invalid. This tells me there is
something going on with the password hash/compare
function.
Can you please guide through the right module to look for this,
Will be quite helpful,
--/Vipin
I have started testing with creating a new user and the password hash
created using new algorithm,
galaxy=# select username,email,password from galaxy_user where email = '
fml...@gmail.com';
username | email | password
--+--+--
| fml...@gmail.com | PBKDF2$sha256$1$e0DVCuGEua3ebxxU$Bh6
I have updated the length of password column to 80 characters in my table
and still the stored password
seems to be in 40 char long, I print the hash after creating the second
hash (password - sha1 hash 40 char long- pbdkf2 hash 69 char long)
before storing into the database table, I believing the hash has
been truncated, any idea what is happening here.
I am not seeing any clue in the code.
thanks, Vipin
Thanks James, I have updated the password of one user in galaxy_user
table with the new algorithm,
I also adjusted the function new_secure_hash
in /lib/galaxy/util/hash_util.py in such a way that it returns
the new hash instead of sha1. Now I tried to login, it fails to get the
account, I think there is something going
wrong in the password hash comparison. Can you please assit here.
+++ b/lib/galaxy/util/hash_util.py Thu May 02 14:33:07 2013 -0400
@@ -25,13 +25,60 @@
Returns either a sha1 hash object (if called with no arguments), or a
hexdigest of the sha1 hash of the argument `text_type`.
+import hashlib
+from os import urandom
+from base64 import b64encode, b64decode
+from itertools import izip
+from pbkdf2 import pbkdf2_bin
+
+SALT_LENGTH = 12
+KEY_LENGTH = 24
+HASH_FUNCTION = 'sha256'
+COST_FACTOR = 1
+
if text_type:
+#return sha1( text_type ).hexdigest()
+
+sec_hash_1 = sha1( text_type ).hexdigest()
+
+if isinstance(sec_hash_1, unicode):
+sec_hash_1 = sec_hash_1.encode('utf-8')
+salt = b64encode(urandom(SALT_LENGTH))
+
+return 'PBKDF2${0}${1}${2}${3}'.format(
+HASH_FUNCTION,
+COST_FACTOR,
+salt,
+b64encode(pbkdf2_bin(sec_hash_1, salt, COST_FACTOR,
KEY_LENGTH, getattr(hashlib, HASH_FUNCTION
thanks, Vipin
That should be the only place, it is called from the some methods of
the User model object. So you could modify it to always hash new
passwords in a different way, but check old passwords with sha1 first,
then something else.
Although it might be nice to move the functionality into
security.validate_user_input since it is really specific to user
passwords, especially with those changes.
I'd be happy to see this go into main with sha256 or something
similar. Also, we could consider adding a random per-user salt field
if you are really concerned about this.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Thu, May 2, 2013 at 10:21 AM, Vipin TS vipin...@gmail.com wrote:
Hello dev-team,
I would like to add the different type of password encryption to the
users
in my galaxy instance. I started working with the current password
encoding
script:
/home/apps/galaxy-dist/lib/galaxy/util/hash_util.py
I will keep the current sha1 and add another layer of encryption to
the sha1
hash, otherwise I need to force all my users to change the password and
follow the new hashing method.
Can anyone please point me any other place/script which I missed
regarding
the encryption/decryption of user authentication.
thanks in advance,
--/Vipin
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Re: [galaxy-dev] redirection vulnerability via URL injection
Thanks Dan! I am not sure about the dataset redirecting places other than ucsc and wormbase genome browser. By now, this can be done through Trackster right? Then I will probably disable the external redirecting. any comments/suggestions. thanks, --/Vipin Hi Vipin, Thank you for reporting this issue. This has to do with the way that the old-style (hard-coded) display applications were modified after introduction of roles to authorize access to an user's datasets that might be permission protected. Ideally, with these old-style applications, much of the work that is being done upfront on history load would be backended to happen after the user clicks to view a dataset -- e.g. the viewport is being generated for all datasets in a history, example link: http://localhost:8080/datasets/190/display_at/ucsc_main?redirect_url=http%3A%2F%2Fgenome.ucsc.edu%2Fcgi-bin%2FhgTracks%3Fdb%3Dhg18%26position%3Dchr21%3A0-536870912%26hgt.customText%3D%25sdisplay_url=http%3A%2F%2Flocalhost%3A8080%2Froot%2Fdisplay_as%3Fid%3D190%26display_app%3Ducsc%26authz_method%3Ddisplay_at If redesigned so that everything happens after the user clicks the link, I see no reason why the redirect_url functionality could not be removed. As it stands now, the redirect url is %s substituted with the URL-encoded value that will contain the authorized URL to access the dataset (e.g. http://localhost:8080/root/display_as?id=190display_app=ucscauthz_method=display_at), and then the user is redirected there. I've added a Trello card (https://trello.com/c/uIctksud) for this issue. In the mean time, however, I have committed a patch to the stable branch that will allow administrators to disable the use of the old-style display applications. Thanks for using Galaxy, Dan On Mar 12, 2013, at 12:08 PM, Vipin TS wrote: Hello dev-members, We are trying to place our public Galaxy instancehttp://galaxy.raetschlab.org/in a more secured manner, Currently I am playing with few test cases about the redirection vulnerabilities. The following link uses a URL variable called “redirect_url” to redirect a user to a given page. While this variable is intended to only direct a user to a trusted page, it fails to validate the provided value and therefore can be used to redirect to any page. http://localhost:8080/datasets/332056/display_at/ucsc_test?redirect_url=http://www.google.comdisplay_url=http://localhost:8080/root This example redirects a user to Google, but it could just as easily be used to direct a user to a page that contains any malware. To resolve the issue, may be validate all user controlled input, including the GET request variables. If the input is intended to redirect a user, it must be validated to ensure it only presents them with a page on the trusted site. any comments or suggestions to work around this. thanks --/Vipin Rätschlab, Computational biology dept. Memorial Sloan-Kettering Cancer Center ___ 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/ ___ 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] best practice to replace the hashing for galaxy-user passwords
Dear dev-team, I am interested to implement the secure hashed password specifically SHA-256 or greater to the galaxy users using publicly available python module PBKDF2. I have a piece of python code which will do the job but not quite sure how I can integrate this to my local galaxy code repository. I saw the current implementation in galaxy/util/hash_util.py any suggestions, thanks, --/Vipin ___ 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] redirection vulnerability via URL injection
Hello dev-members, We are trying to place our public Galaxy instancehttp://galaxy.raetschlab.orgin a more secured manner, Currently I am playing with few test cases about the redirection vulnerabilities. The following link uses a URL variable called “redirect_url” to redirect a user to a given page. While this variable is intended to only direct a user to a trusted page, it fails to validate the provided value and therefore can be used to redirect to any page. http://localhost:8080/datasets/332056/display_at/ucsc_test?redirect_url=http://www.google.comdisplay_url=http://localhost:8080/root This example redirects a user to Google, but it could just as easily be used to direct a user to a page that contains any malware. To resolve the issue, may be validate all user controlled input, including the GET request variables. If the input is intended to redirect a user, it must be validated to ensure it only presents them with a page on the trusted site. any comments or suggestions to work around this. thanks --/Vipin Rätschlab, Computational biology dept. Memorial Sloan-Kettering Cancer Center ___ 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/
Re: [galaxy-dev] Serving Galaxy behind apache mod_security
Hello Paul, Due to various security issues, we thought to run our instance (will be public soon) behind apache web server. It seems that the SELinux is disabled on my machine. I have followed the steps and restarted apache, still not able to invoke the Galaxy page through http://servername:8080/ Thanks, --/Vipin Rätschlab, Computational biology dept. Memorial Sloan-Kettering Cancer Center On Tue, Mar 12, 2013 at 8:15 AM, Paul Boddie paul.bod...@biotek.uio.nowrote: On 11/03/13 23:20, Vipin TS wrote: On my new server machine I have configured apache server along with mod_security. Now I would like to place my Galaxy installation behind apache and is there any detailed explanation to describes the steps. I am following the galaxy wiki pagehttp://wiki.**galaxyproject.org/Admin/**Config/Apache%20Proxy#http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy# and it is failing to invoke the page. Please share if you have an experience on the same. I have avoided experience with Galaxy and mod_proxy (and once again wonder why mod_wsgi wouldn't be a better and less complicated way of running Galaxy, but that's another issue), but I do have experience with mod_proxy and other solutions that need their own Web server, and I notice that the Wiki page doesn't contain any mention of SELinux. If you have everything set up appropriately, you may need to find out whether SELinux is enabled, because this may demand a small amount of additional configuration work. Paul ___ 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/
[galaxy-dev] Serving Galaxy behind apache mod_security
Hello members, On my new server machine I have configured apache server along with mod_security. Now I would like to place my Galaxy installation behind apache and is there any detailed explanation to describes the steps. I am following the galaxy wiki pagehttp://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy# and it is failing to invoke the page. Please share if you have an experience on the same. thanks in advance, --/Vipin ___ 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/
[galaxy-dev] Authentication: email addresses are not validated prior to account creation
Hello members, I believe currently there is no process to validate email address provided during user account creation. We are experiencing a huge fake account creation attack on our public facing galaxy instancehttp://galaxy.raetschlab.org . Does anybody who has been managing a public instance, implemented an on-demand account creation activation by sending an email containing a link, which when clicked, validate the account creation request. Or any plans from dev-team to add this in future release? thanks in advance, --/Vipin ___ 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/
[galaxy-dev] single database connection and multiple Galaxy instance
Hi Galaxy team, Can I use a single database connection to serve multiple Galaxy instance ? thanks, --Vipin ___ 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/
Re: [galaxy-dev] How to get admin account on Galaxy
on your local instance, please read the following: http://wiki.g2.bx.psu.edu/Admin/Interface --Vipin On 24 August 2012 13:09, kauerb...@comcast.net wrote: Hello, Can you tell me how to become an 'admin' user on Galaxy, or else change the current admin? Thank you. -Ken. ___ 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/ ___ 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/
[galaxy-dev] Galaxy Tool Shed upload error
Hi Galaxy team, I am trying to upload a tool wrapper to main tool shed http://toolshed.g2.bx.psu.edu and ending up with a 'server error' message. Could you please let me know what is going wrong here. thanks, --Vipin ___ 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/
Re: [galaxy-dev] R scripts for DESeq
Hi Carlos,
Currently I am in a transition period, and I didn't get much time to look
on the same, Sorry for the delay.
For getting the read count, we wrote script and which is wrapped in Deseq
main program.
regards,
--Vipin T S
On 26 March 2012 14:01, Carlos Borroto carlos.borr...@gmail.com wrote:
Hi Vipin,
I was wondering if there is any progress on getting your DESeq wrapper
into the Tool Shed? I'm also highly interested on using DESeq inside
Galaxy.
Also, what you use for generating the read counts for DESeq? Do you
produce these counts inside Galaxy?
Thanks,
Carlos
On Thu, Feb 23, 2012 at 4:46 AM, Vipin TS vipin...@gmail.com wrote:
Hi Chris,
We are running DESEQ_VERSION 1.6.0 at our instance
http://galaxy.tuebingen.mpg.de/tool_runner?tool_id=deseq
thanks,
--Vipin T S
Which version of DESeq does this tool use?
Note that there are significant differences between DESeq 1.4 (the
version
described in the paper) and 1.6.x (current release). The differences are
both in functionality and results.
Regards,
Chris
On 23/02/2012 02:27, Greg Von Kuster g...@bx.psu.edu wrote:
Lisa,
In case you aren't aware, you can set your user preferences for your
account in the tool shed to receive an email message when a new
repository's first upload occurs. This would keep you from having to
check the tool shed. Go to User - Preferences - Manage
your email alerts and you'll see the following setting.
On Feb 22, 2012, at 8:50 PM, Liusong Yang wrote:
Hi Vipin,
That is a wonderful news and I am eager to see it in tool shed. I am
going to check tool shed frequently these days to get it asap.
Thanks
Lisa
On Wed, Feb 22, 2012 at 4:07 PM, Vipin TS vipin...@gmail.com
wrote:
Hi,
We have the recent release version of DESeq at our Galaxy instance,
http://galaxy.tuebingen.mpg.de/tool_runner?tool_id=deseq
I will add the Galaxy wrapper for DESeq in community tool shed in
few
days.
regards,
--Vipin
Hi Lisa,
I am going to send your question over to the galaxy-...@bx.psu.edu
mailing
list so that the development community can offer feedback.
http://wiki.g2.bx.psu.edu/Support#Starting_a_technical.2C_local.2BAC8-clou
d_instance.2C_or_development_thread
http://wiki.g2.bx.psu.edu/Support#Starting_a_technical.2C_local.2BAC8-clo
ud_instance.2C_or_development_thread
Th galaxy-user list is primarily for tool/data usage on the Galaxy
public
server.
http://wiki.g2.bx.psu.edu/Mailing%20Lists
Thanks,
Jen
Galaxy team
Original Message
Subject: [galaxy-user] R scripts for DESeq
Date: Tue, 21 Feb 2012 23:25:35 -0500
From: Liusong Yang liusongyang2...@gmail.com
To: galaxy-u...@lists.bx.psu.edu
Hello,
I am planning to put DESeq into galaxy. I am a newcomer for both
Galaxy and R. I have already read all of the related discussion in
this group. I also noticed that there are r_wrapper.sh and
DESeq.xml
added into galaxy recently under the path of tools.
These lines are from r_wrapper.sh.
### Run R providing the R script in $1 as standard input and
passing
### the remaining arguments on the command line
I guess this means we need to give the DESeq R script to the
wrapper
as standard input. My question is where or what is the DESeq R
scripts? I installed R and DESeq package, but I can not fund
anything
like DESeq.R or something similar? I feel so confusing now. Any
comments or suggestions would be absolutely appreciated!
Thanks
Lisa
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Re: [galaxy-dev] Restrict tool usage by certain users
Hi Daniel,
On 22 March 2012 08:20, Daniel Sobral dsob...@igc.gulbenkian.pt wrote:
Hello,
At the moment I don't think there is a way to restrict usage of specific
tool(s) to specific user(s).
Is anyone thinking on developing this kind of functionality?
I guess it might be a bit complicated to implement?
I guess an easier alternative is to have different galaxy instances
running, each one with a different tool set?
Instead of running multiple instances I would recommend you to add few
lines of code in your tool configuration file (.xml)
1. Export the $__user_email__ variable along with the tool call section in
XML file.
ex:
command/path-to-tool/wrapper.sh ARG1 ARG2 ... $__user_email__
/command
2. In the wrapper.sh script, add the following line in the before calling
your main program.
if [ ${@: -1} != vipin...@gmail.com ];
then
echo 'You donot have enough privilege to access this tool, please
contact gal...@tuebingen.mpg.de'
exit
fi
By doing this way the tool name will be listed in the tool panel of Galaxy
instance, but for this specified
user can only access the same. I know this is not an automated way of
implementation and happy to hear
if somebody have another fix for the same.
I implemented this in my public Galaxy instance and it is accessible
herehttp://galaxy.fml.mpg.de/tool_runner?tool_id=rquant_web
.
HTH, Vipin
Thanks,
Daniel
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Re: [galaxy-dev] R scripts for DESeq
Hi Chris, We are running DESEQ_VERSION 1.6.0 at our instance http://galaxy.tuebingen.mpg.de/tool_runner?tool_id=deseq thanks, --Vipin T S Which version of DESeq does this tool use? Note that there are significant differences between DESeq 1.4 (the version described in the paper) and 1.6.x (current release). The differences are both in functionality and results. Regards, Chris On 23/02/2012 02:27, Greg Von Kuster g...@bx.psu.edu wrote: Lisa, In case you aren't aware, you can set your user preferences for your account in the tool shed to receive an email message when a new repository's first upload occurs. This would keep you from having to check the tool shed. Go to User - Preferences - Manage your email alerts and you'll see the following setting. On Feb 22, 2012, at 8:50 PM, Liusong Yang wrote: Hi Vipin, That is a wonderful news and I am eager to see it in tool shed. I am going to check tool shed frequently these days to get it asap. Thanks Lisa On Wed, Feb 22, 2012 at 4:07 PM, Vipin TS vipin...@gmail.com wrote: Hi, We have the recent release version of DESeq at our Galaxy instance, http://galaxy.tuebingen.mpg.de/tool_runner?tool_id=deseq I will add the Galaxy wrapper for DESeq in community tool shed in few days. regards, --Vipin Hi Lisa, I am going to send your question over to the galaxy-...@bx.psu.edu mailing list so that the development community can offer feedback. http://wiki.g2.bx.psu.edu/Support#Starting_a_technical.2C_local.2BAC8-clou d_instance.2C_or_development_thread http://wiki.g2.bx.psu.edu/Support#Starting_a_technical.2C_local.2BAC8-clo ud_instance.2C_or_development_thread Th galaxy-user list is primarily for tool/data usage on the Galaxy public server. http://wiki.g2.bx.psu.edu/Mailing%20Lists Thanks, Jen Galaxy team Original Message Subject: [galaxy-user] R scripts for DESeq Date: Tue, 21 Feb 2012 23:25:35 -0500 From: Liusong Yang liusongyang2...@gmail.com To: galaxy-u...@lists.bx.psu.edu Hello, I am planning to put DESeq into galaxy. I am a newcomer for both Galaxy and R. I have already read all of the related discussion in this group. I also noticed that there are r_wrapper.sh and DESeq.xml added into galaxy recently under the path of tools. These lines are from r_wrapper.sh. ### Run R providing the R script in $1 as standard input and passing ### the remaining arguments on the command line I guess this means we need to give the DESeq R script to the wrapper as standard input. My question is where or what is the DESeq R scripts? I installed R and DESeq package, but I can not fund anything like DESeq.R or something similar? I feel so confusing now. Any comments or suggestions would be absolutely appreciated! Thanks Lisa ___ 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/ ___ 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/ ___ 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/ ___ 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/ The University of Dundee is a registered Scottish Charity, No: SC015096 ___ 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/ ___ 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/
Re: [galaxy-dev] Shogun Toolbox?
Dear Kipper, We are running most of our tools with the help of Shogun toolbox. Just configure a recent version of Shogun toolbox to your local machine and add the python path to your program. By doing this you will be able to call shogun functionalities in your programs. (Depends on the configuring path you will be able to find the shared object file and main library files) Recent version of shogun can be find at ftp://shogun-toolbox.org/shogun/releases/1.0/sources/shogun-1.0.0.tar.bz2 HTH, Vipin Friedrich Miescher Laboratory of the Max Planck Society Spemannstrasse 39, 72076 Tuebingen, Germany Dear List, I am new to developing for Galaxy and haven't found a good answer to this question yet. Does Galaxy Test Toolshed use or recognize Shogun Toolbox ( http://www.shogun-toolbox.org/)? I'm considering writing a module for Galaxy, but the underlying Python code relies on Shogun, and I haven't seen a suppported 3rd party software list, so I can't tell if Galaxy would be able to run the module without my rewriting it not to depend on Shogun. Thank you, Kipper Fletez-Brant ___ 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/ ___ 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/
Re: [galaxy-dev] Shogun Toolbox?
Hi Kipper, Sorry I got confused, Yes you are right, both ways are fine I think. --Vipin Vipin, Thanks for quick reply. Pardon my asking, as I said I am new to Galaxy development, but if I wanted to share my module, would other users need to install Shogun separately, or could I include it as a dependency or 'egg'? On Nov 28, 2011, at 2:28 PM, Vipin TS vipin...@gmail.com wrote: Dear Kipper, We are running most of our tools with the help of Shogun toolbox. Just configure a recent version of Shogun toolbox to your local machine and add the python path to your program. By doing this you will be able to call shogun functionalities in your programs. (Depends on the configuring path you will be able to find the shared object file and main library files) Recent version of shogun can be find at ftp://shogun-toolbox.org/shogun/releases/1.0/sources/shogun-1.0.0.tar.bz2 HTH, Vipin Friedrich Miescher Laboratory of the Max Planck Society Spemannstrasse 39, 72076 Tuebingen, Germany Dear List, I am new to developing for Galaxy and haven't found a good answer to this question yet. Does Galaxy Test Toolshed use or recognize Shogun Toolbox ( http://www.shogun-toolbox.org/)? I'm considering writing a module for Galaxy, but the underlying Python code relies on Shogun, and I haven't seen a suppported 3rd party software list, so I can't tell if Galaxy would be able to run the module without my rewriting it not to depend on Shogun. Thank you, Kipper Fletez-Brant ___ 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/ ___ 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/
Re: [galaxy-dev] Does Galaxy have a tool to run R script?
Dear all,
I want to build a Galaxy tool to run R script.
Do you know if there is already such tool or similar function?
If you can share with me, I would very appreciate your help.
Hi Bo Liu,
In my Galaxy instance I added few tools running with R. Here I just wrote a
bash wrapper script to run the R program.
Something like this:
a) tool.xml file
command
/home/foo/tools/deseq/src/deseq.sh $anno_input.select_anno_format
$anno_out $deseq_out $bam_alignments1 $bam_alignments2
$Log_File
/command
b) deseq.sh file
## calling R script
cat ../src/difftest_deseq.R | /usr/bin/R --slave --args $tmpfile
${DESEQ_RES}
Hope this will solve your issue !
--Vipin
Thank you,
Bo Liu
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Re: [galaxy-dev] fyi: can't upload to toolshed
Server ErrorAn error occurred. See the error logs for more information. (Turn debug on to display exception reports here) My guess is that this will be a problem with your tool configuration file in XML format. -- Vipin ___ 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/
Re: [galaxy-dev] BAM display at Trackster
Hi Jeremy, Sorry for the delayed response from my side. (1) click the pencil on a BAM dataset; (2) try converting from BAM to BAI; If the conversion failed, you should receive an informative error message about why it's failing. Once you get this conversion to pass, you should be able to visualize your BAM dataset in Trackster. Thanks for your suggestions and they helped me to debug the issue. The conversion from BAM to BAI was working fine at my end. After few hours of debugging I had found that the error was caused by a mistake from my side, the BAM file which I tried to display on trackster was corrupted. Many thanks for your quick replies, Also I have a request about a search option in Trackster (We discussed at GCC) It will be great if you would enable a search option such that biologist/user can look for a particular feature based on feature ID or Name, (for example: read coverage for a candidate gene) Right now user need to go through all regions over the chromosomes. In my point most of users are more familiar with names than location in the genome. Thanks for considering, --Vipin Let us know if you're still having trouble. Best, J. ___ 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/
Re: [galaxy-dev] BAM display at Trackster
Hi Jeremy, Are you able to visualize any BAM files in Trackster or do all files fail with the same error? Were you able to visualize BAM files before you updated your instance? Do you have SAMTools--which is required by Trackster--installed and available via your path? Yes, all BAM fails are failing with the same error message. Before updating my instance I did not try to visualize through Trackster. Samtools path are available to Galaxy. I am not seeing any error/warning message in my log file. Thanks for your consideration --Vipin ___ 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/
Re: [galaxy-dev] BAM display at Trackster
Hi Kanwei, Is this from a recent changeset that you pulled? Yes I pulled on yesterday (6-7-2011) --Vipin ___ 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/
[galaxy-dev] BAM display at Trackster
Hi Galaxy team, I am experiencing a problem with visualizing my BAM files through Trackster at my Galaxy instance. Please find the attached image along with this mail. From the log file I am not seeing any clues about the error message which is displayed on my browser page (A dependency (bai) was in an error state.) I updated my instance recently, It will be great if you can help me on the same. Thanks in advance, Vipin Friedrich Miescher Laboratory of the Max Planck Society Tuebingen attachment: trackster_image_vipin.png___ 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/
Re: [galaxy-dev] Restoring galaxy database return few empty tables.
Hello Nate, When restoring, I generally use the --disable-triggers, which instructs Postgres to ignore foreign key constraints. --nate Sorry for the relayed response from my side. As you suggested I tried with --disable-triggers option for restoring the database from the dump file, Apparently this returns some notice message associated with circular foreign-key constraints for few tables. Here are some notice messages: pg_dump: NOTICE: there are circular foreign-key constraints among these table(s): pg_dump: stored_workflow pg_dump: workflow pg_dump: You may not be able to restore the dump without using --disable-triggers or temporarily dropping the constraints. pg_dump: Consider using a full dump instead of a --data-only dump to avoid this problem. and finally ended up with: pg_dump: Consider using a full dump instead of a --data-only dump to avoid this problem. pg_restore: [archiver (db)] Error while PROCESSING TOC: pg_restore: [archiver (db)] Error from TOC entry 3075; 0 16650 TABLE DATA history_dataset_association galaxy pg_restore: [archiver (db)] COPY failed: ERROR: invalid byte sequence for encoding UTF8: 0xb9 HINT: This error can also happen if the byte sequence does not match the encoding expected by the server, which is controlled by client_encoding. CONTEXT: COPY history_dataset_association, line 8149 pg_restore: [archiver (db)] Error from TOC entry 3064; 0 16435 TABLE DATA job galaxy pg_restore: [archiver (db)] COPY failed: ERROR: invalid byte sequence for encoding UTF8: 0xb9 HINT: This error can also happen if the byte sequence does not match the encoding expected by the server, which is controlled by client_encoding. CONTEXT: COPY job, line 16578 WARNING: errors ignored on restore: 2 Based on the suggestions from the error and notice message first one seems to be not much harm to the database contents. I believe the second one points to some naming related thing, other than that I don't have much idea. According to the above suggestions I tried to load the dump files directly and it also ended up with error message. from the man page I understood that pg_restore will use the option --disable-triggers with --data-only dump. My issue is not yet solved, that is the 'job' table seems to be empty. Please let me know if I am doing something wrong. Here is my inputs, dumping table schema pg_dump --schema --create -F t --host MAN | pg_restore --dbname=galaxy -F t dumping table contents pg_dump --data-only --create -F t --host MAN | pg_restore --dbname=galaxy -F t --disable-triggers Many thanks for your suggestions, Vipin ___ 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/
Re: [galaxy-dev] Restoring galaxy database return few empty tables.
Hello Nate, Can you make sure that your dump was created with '-E UTF-8' flag? I didn't use any customized encoding for my dump, took the default one, I believe which is the database encoding. Also, in your old database server, use psql's '\l' command to show the encoding of your databases. My database encoding is SQL_ASCII thanks, Vipin ___ 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/
[galaxy-dev] Restoring galaxy database return few empty tables.
Dear Galaxy Team, I am switching our Galaxy production service to a new machine, We are using Postgres as database server. The existing database belongs to postgres version 8.3 and I took my instance's dump using postgres version 8.4. I am able to restore my database on postgres 8.4, Except few tables were empty and with few strange error message left on log file. I am not sure how many tables are empty, but I found table called 'job' returns 0 rows. Original job table returns me 40733 rows. excerpts from error log: ERROR: insert or update on table history_dataset_association_annotation_association violates foreign key constraint history_dataset_association_a_history_dataset_association__fkey DETAIL: Key (history_dataset_association_id)=(284985) is not present in table history_dataset_association. STATEMENT: ALTER TABLE ONLY history_dataset_association_annotation_association ADD CONSTRAINT history_dataset_association_a_history_dataset_association__fkey FOREIGN KEY (history_dataset_association_id) REFERENCES history_dataset_association(id); ERROR: insert or update on table history_dataset_association_tag_association violates foreign key constraint history_dataset_association_t_history_dataset_association__fkey DETAIL: Key (history_dataset_association_id)=(387932) is not present in table history_dataset_association. STATEMENT: ALTER TABLE ONLY history_dataset_association_tag_association In my knowledge we didn't do any manual transactions on Galaxy database and Could anyone let me know something wrong at my end. I'm sure this has been covered somewhere but I haven't been able to find it on the Wiki or by searching the archives. Thanks in advance, Vipin Friedrich Miescher Laboratory of the Max Planck Society Spemannstrasse 39, 72076 Tuebingen, Germany ___ 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/
Re: [galaxy-dev] bwa failure preparing job
Hi Branden, Vipin, thanks for the tip. I was not aware of data tables at all. I checked bwa_wrapper.xml and it is still using the from_file attribute for the reference genome parameter, not from_data_table. It would appear then that BWA is not using data tables? Additionally, I have now noticed that our bowtie runs are failing as well with the error: I am not sure about the below error message, based on the previous mail error message it is cleat that it is looking for a data_table type value instead of from_file. I hope something will be broken at your end when you pulled at last time. AssertionError: Requested 'path' column missing from column def I looked at bowtie_wrapper.xml, and it too seems to still be using from_file instead of from_data_table for the reference genome drop-down. There is a line there using data tables, but it is commented out: !--options from_data_table=bowtie_indexes/-- I'm really confused as to what is going on here, but it seems like when I updated recently (first time since January probably) it broke all of my location files and I'm not sure how to fix them. I'm also confused because it seems that even using data tables, the format of my .loc files shouldn't need to change because they both use four columns separated by tabs. As always, any help is greatly appreciated. I think probably the best idea to move everything to data_table based on the documentation available in the Wiki page. Galaxy also recommending the same. If I found something useful, I will share with you. regards, Vipin ___ 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/
Re: [galaxy-dev] bwa failure preparing job
Hi Branden, I find a wiki documentation here, https://bitbucket.org/galaxy/galaxy-central/wiki/DataTables Hope this will help you to experiment a bit around. regards, Vipin Does anybody have any idea why I would be getting this error before the tool runs? -- Branden Timm Great Lakes Bioenergy Research Center bt...@wisc.edu On 4/19/2011 10:45 AM, Branden Timm wrote: Hi All, I'm having issues running BWA for Illumina with the latest version of Galaxy (5433:c1aeb2f33b4a). It seems that the error is a python list error while preparing the job: Traceback (most recent call last): File /home/galaxy/galaxy-central/lib/galaxy/jobs/runners/local.py, line 58, in run_job job_wrapper.prepare() File /home/galaxy/galaxy-central/lib/galaxy/jobs/__init__.py, line 371, in prepare self.command_line = self.tool.build_command_line( param_dict ) File /home/galaxy/galaxy-central/lib/galaxy/tools/__init__.py, line 1575, in build_command_line command_line = fill_template( self.command, context=param_dict ) File /home/galaxy/galaxy-central/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File /home/galaxy/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py, line 1004, in __str__ return getattr(self, mainMethName)() File DynamicallyCompiledCheetahTemplate.py, line 106, in respond IndexError: list index out of range I checked the bwa_index.loc file for errors, it seems that the line for the reference genome I'm trying to map against is correct (all whitespace is tab characters): synpcc7002 synpcc7002 Synechococcus /home/galaxy/galaxy-central/bwa_ indices/SYNPCC7002 I'm not sure what the next troubleshooting step is, any ideas? -- Branden Timm bt...@glbrc.wisc.edu ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] Question on finding external_filename and _extra_files_path from psql DB.
Hi Dannon, Thanks for pointing the same. Vipin, The numerical portion of the file path is not saved in the database, rather it is generated on the fly by the function directory_hash_id in lib/galaxy/model/__init__.py. The filename itself should be named in the format dataset_dataset id.dat. So, using that directory_hash_id function, you should be able to reconstruct the full path to the file on disk with just the unencoded dataset id and the root galaxy files directory prefix. -Dannon On Apr 25, 2011, at 4:16 PM, Vipin TS wrote: Dear Galaxy Team, As a part of in-house automated cleaning of data set from our production galaxy service, I am finding difficulty to get the galaxy assigned file name (galaxy-root/database/001/dataset_001.dat) for each data set from the corresponding database. We are using PostgreSQL and when I queried through the table name called 'dataset', couldn't figure out the values for external_filename or _extra_files_path. For example: select * from dataset order by id DESC limit 10; id |create_time |update_time | state | deleted | purged | purgable | external_filename | _extra_files_path | file_size 70805 | 2011-04-22 20:49:55.319709 | 2011-04-22 20:50:26.643807 | ok | f | f | t| | | 421593 Could you please let me know where I can locate the file name from other tables or do I need to set up any configuration. Thanks in advance, Vipin Friedrich Miescher Laboratory of the Max Planck Society Spemannstrasse 39, 72076 Tuebingen, Germany ___ 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/ ___ 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/
[galaxy-dev] Question on finding external_filename and _extra_files_path from psql DB.
Dear Galaxy Team, As a part of in-house automated cleaning of data set from our production galaxy service, I am finding difficulty to get the galaxy assigned file name (galaxy-root/database/001/dataset_001.dat) for each data set from the corresponding database. We are using PostgreSQL and when I queried through the table name called 'dataset', couldn't figure out the values for external_filename or _extra_files_path. For example: select * from dataset order by id DESC limit 10; id |create_time |update_time | state | deleted | purged | purgable | external_filename | _extra_files_path | file_size 70805 | 2011-04-22 20:49:55.319709 | 2011-04-22 20:50:26.643807 | ok | f | f | t| | | 421593 Could you please let me know where I can locate the file name from other tables or do I need to set up any configuration. Thanks in advance, Vipin Friedrich Miescher Laboratory of the Max Planck Society Spemannstrasse 39, 72076 Tuebingen, Germany ___ 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/
Re: [galaxy-dev] Galaxy Tool Shed:- Uploading tool packages fails with Server Error message
Hi Greg, Regarding the tools contained in fml_gff_converter_programs.tar.bz2, the following xml files are not well formed due to the malformed ! -- TODO EDIT HERE tag: fml_gff_converter_programs/galaxy/bed_to_gff3.xml fml_gff_converter_programs/galaxy/gff3_to_bed.xml fml_gff_converter_programs/galaxy/gff3_to_gtf.xml fml_gff_converter_programs/galaxy/gtf_to_gff3.xml In addition, none of these files include the required version attribute in the tool tag. Many thanks for pointing me the version number issue with tool configuration file. I forgot the same. The same goes for the files in ~/gff_groomer/fml_gff_groomer/galaxy - they are not well-formed due to the same ! -- TODO EDIT HERE tag, and they do not include the version attribute int the tool tag. Tools tags should look something like this: tool id=fml_bed2gff name=BED_to_GFF3 version=1.0.0 I've made some enhancements to the tool shed code that will display errors like this ( rather than resulting in the current server error ), so the next time I update the tool shed ( within the next couple of days ), this problem will be corrected. In the meantime, if you make the above corrections, you should have no problems uploading your tools to the tool shed. Thanks very much for pointing out these issues, and for taking the time to contribute your tools to the Galaxy community. Yes I did the changes accordingly and now it uploaded into the Tool shed. Thanks for your quick fix. regards, Vipin ___ 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/
[galaxy-dev] Galaxy Tool Shed:- Uploading tool packages fails with Server Error message
Dear Galaxy team, I would like to upload a set of converter programs available for Generic Feature Format (GFF). When I tried to upload to Galaxy tool shed using my user name vipin...@tuebingen.mpg.de, it gives me Server error message. I am using a *.bz2 file for uploading. It will be great if you can have a look on this issue. thanks in advance, Vipin T S Friedrich Miescher Laboratory of the Max Planck Society Spemannstrasse 39, 72076 Tuebingen, Germany Tel:+49 7071 601 824 ___ 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/
