- galaxy-dev - lists.galaxyproject.org

Trouble with async data sources
by Eric Rasche 30 Dec '14

30 Dec '14

1 0

inconsistency in data library display
by Ryan G 24 Dec '14

24 Dec '14

I'm uploading a bunch of fastq.gz files to a data library. I'm currently doing this one file at a time to test some API functionality. I noticed that right after the web page refreshes itself, the file name is displayed with a '.gz' at the end. If I navigate to the data library by clicking on 'Manage Data Libraries", etc, the file is displayed without the '.gz'. Not a big deal, but it was throwing me off for a while trying to figure out how to use the underlying API.

1 1

Feature Request: Ability to you keyword to move through items in the main window similar to Gmail
by Ryan G 23 Dec '14

23 Dec '14

When browsing a data library, clicking on entries I want to select is a bit cumbersome. It would be nice to use arrow keys, etc to select items, just like when selecting mail in Gmail.

2 3

rpy vs rpy2
by Ryan G 22 Dec '14

22 Dec '14

I'm trying to install rpy for Galaxy, however it seems to not be available anymore. rpy2 is supposed to be the replacement. Does/will Galaxy migrate to rpy2? Some of the tools rely on rpy but since its not available anymore, the tools can't run. Also, why use a R python wrapper? Why not just create an R script and run 'Rscript' directly? Ryan

2 2

Create a package with binaries
by KRESS Arnaud (ESP) 22 Dec '14

22 Dec '14

Hi gentlemen, I am currently struggling to create a custom package (to share via a toolshed) that would include a tool definition file and the associated binary. Once installed, I can launch a job but I get the following error message: mytool.sh: line 14: mytool: unknown command It seems that the PATH was not correctly set. What am I doing wrong ? My directory tree in my package: . ├── mytool.sh ├── mytool.xml ├── bin │ └── mytool └── tool_dependencies.xml Here is my tool_dependencies.xml file content: <?xml version="1.0"?> <tool_dependency> <package name="mytool" version="1.0"> <install version="1.0"> <actions> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> </readme> </package> </tool_dependency> Thank you, AK

3 4

Problem with LWR (input size limitation)
by Misharl Monsoor 22 Dec '14

22 Dec '14

Hi everybody, In our lab, we are trying to connect our Galaxy instance to a Windows 7 64 bits server, in order to executes programs that need to be run within Windows. However we have a problem concerning the size of the input that is uploaded to the Windows server, it doesn't accept inputs with a size > 1.3 Gb ? We have the following problem with mmap function: data = mmap.mmap(input.fileno(), 0, access=mmap.ACCESS_READ) error: [Errno 12] Cannot allocate memory I have another question concerning the inputs, is there a way to use several inputs that be uploaded to a Windows Server? Thank you very much in advance, Bests regards, Cheers, Misharl Monsoor

2 8

Metadata error in uploading files to data libraries
by Jelle Scholtalbers 19 Dec '14

19 Dec '14

Hi all, after an update to the following changeset(14859:7ba05957588a, stable, 05.12.14), our bam files that are uploaded(linked) to a data library, are no longer indexed. The metadata_xxx.dat is created, but it stays empty. The following error message appears in the log, although the state of the dataset is 'ok': galaxy.jobs WARNING 2014-12-05 12:47:02,218 Error accessing /g/K/K27.bam, will retry: [Errno 1] Operation not permitted: '/g/K/K27.bam' galaxy.jobs WARNING 2014-12-08 13:38:57,045 Error accessing /g/K/K2.bam, will retry: [Errno 1] Operation not permitted: '/g/K/K2.bam' All file permissions are correct (i.e. galaxy owns them). Furthermore, executing samtools index, just works on those files: samtools index /g/K/K2.bam /g/galaxy/galaxy_data/files/_metadata_files/006/metadata_6598.dat When uploading the file - "copy files into galaxy" - the samtools index just works. ============== Now, on a clean local install(14874:885f940bff64, stable, 05.12.14) and samtools installed globally and with the bam file sorted, I get the following situation: When I try to upload this bam to a data library by linking the following error is shown on the dataset (note: here the dataset is set in error state, which does not happen on our server) Uploaded by: scholtal(a)embl.de Date uploaded: Mon Dec 8 17:42:39 2014 (UTC) File size: 2.6 GB UUID: d23cf11a-0372-41cb-939a-7c8761d78b73 Data type: auto Build: ? Miscellaneous information: Traceback (most recent call last): File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 407, in __main__() File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 396, in _ Job Standard Error Traceback (most recent call last): File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 407, in __main__() File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 396, in __main__ add_file( dataset, registry, json_file, output_path ) File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 294, in add_file if datatype.dataset_content_needs_grooming( dataset.path ): File "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py", line 147, in dataset_content_needs_grooming version = self._get_samtools_version() File "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py", line 129, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1308, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory error Database/Build: ? Number of data lines: None Disk file: /Users/scholtalbers/workspace/idr_data/WT1.sort.bam =============================== When uploading the bam without linking, I see the following processes: Upload->set meta->samtools index->'error state' Miscellaneous information: uploaded bam file Traceback (most recent call last): File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 407, in __main__() File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.p Job Standard Error Traceback (most recent call last): File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 407, in __main__() File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 396, in __main__ add_file( dataset, registry, json_file, output_path ) File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 324, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py", line 147, in dataset_content_needs_grooming version = self._get_samtools_version() File "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py", line 129, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1308, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory error Database/Build: ? Number of data lines: None Disk file: /Users/scholtalbers/workspace/galaxy-dist-new/database/files/000/dataset_6.dat ================================= Although the error messages are different, it might be related? Cheers, Jelle

2 4

Re: [galaxy-dev] Allow wildcards in upload files from filesystem paths
by Ryan G 19 Dec '14

19 Dec '14

Thanks. It would be a nice feature. I don't have write permissions on the filesystem where the fastq files are stored. On Thu, Dec 18, 2014 at 4:08 PM, Martin Čech <emulatorer(a)gmail.com> wrote: > > Wildcards are not supported in library upload. Sorry. > > You can either specify one by one or you can just move the .log files > outside of a folder for a bit. Once the fastqs are uploaded you can move > them back. > > Martin > > On Thu Dec 18 2014 at 3:46:30 PM Ryan G <ngsbioinformatics(a)gmail.com> > wrote: > >> I have a directory with a bunch of fastq files mixed with .log files. I >> only want to upload the .fastq files. Do I have to specify each fastq file >> separately or can I use '*.fastq'? I tried the later, but got the error >> 'Invald paths'. >> ___________________________________________________________ >> 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: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > >

1 0

Job wrapper object
by Alexandre Defelicibus 18 Dec '14

18 Dec '14

Hi all, I'm developing some tools on my Galaxy instance and I need to get some information about the job that a tool creates. The question is, how can I have a job_wrapper object in my tool wrapper? I tried to use the reserved variable $__app__, but I got errors. I couldn't import and use the galaxy lib in order to get the job information. Could someone show me the correct way to do that, with some examples? I appreciate all the help. Best regards, -- Alexandre Defelicibus Mestrando em Bioengenharia Programa de Pós-Graduação em Bioengenharia Universidade de São Paulo - USP

3 4

Allow wildcards in upload files from filesystem paths
by Ryan G 18 Dec '14

18 Dec '14

I have a directory with a bunch of fastq files mixed with .log files. I only want to upload the .fastq files. Do I have to specify each fastq file separately or can I use '*.fastq'? I tried the later, but got the error 'Invald paths'.

2 1