- galaxy-dev - lists.galaxyproject.org

Determining datatype inheritance in tool XML Cheetah
by Peter Cock 12 Aug '14

12 Aug '14

Hi all, I've just uploaded a simple sequence composition tool to the Test Tool Shed: https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_composition https://github.com/peterjc/pico_galaxy/commit/45669446f5a14fd90a8a0d9d74304… This accepts multiple input in FASTA, FASTQ, or SFF format - and allows a mixture of these: <inputs> <param name="input_file" type="data" format="fasta,fastq,sff" multiple="true" label="Sequence file" help="FASTA, FASTQ, or SFF format." /> </inputs> In order to build the command line string, I am currently using this for loop: <command interpreter="python"> seq_composition.py -o "$output_file" ##For loop over inputs #for i in $input_file --$i.ext "${i}" #end for </command> This results in things like this being run: seq_composition.py -o XXX.dat --fastqsanger XXX.dat --sff XXX.dat This works, but means my Python script has to know about not just the core data types that I specified in my input parameter XML (fasta,fastq,sff) but also any subclasses (e.g. fastqsanger). It seems what I want/need would be something along these lines in pseudo-code to map any datatype which is a subclass for fastq to use a single command line option: <command interpreter="python"> seq_composition.py -o "$output_file" ##For loop over inputs #for i in $input_file #if isinstance($i.datatype, fastq): --fastq "${i}" #else --$i.ext "${i}" #end if #end for </command> This mock example borrows from the Python isinstance function, but of course some Galaxy datatypes are defined as subclasses at the XML level rather than literally at the Python class level. This should result in getting the following regardless of which flavour of FASTQ the input dataset had assigned: seq_composition.py -o XXX.dat --fastq XXX.dat --sff XXX.dat Does anyone have any Tool XML examples probing an input file's datatype in this way? Peter

2 2

bug?
by Langhorst, Brad 12 Aug '14

12 Aug '14

I see this in my database server logs… SELECT history_dataset_association.id AS history_dataset_association_id, history_dataset_association.history_id AS history_dataset_association_history_id, history_dataset_association.dataset_id AS history_dataset_association_dataset_id, history_dataset_association.create_time AS history_dataset_association_create_time, history_dataset_association.update_time AS history_dataset_association_update_time, history_dataset_association.state AS history_dataset_association_state, history_dataset_association.copied_from_history_dataset_association_id AS history_dataset_association_copied_from_history_dataset_a_1, history_dataset_association.copied_from_library_dataset_dataset_association_id AS history_dataset_association_copied_from_library_dataset_d_2, history_dataset_association.hid AS history_dataset_association_hid, history_dataset_association.name AS history_dataset_association_name, history_dataset_association.info AS history_dataset_association_info, history_dataset_association.blurb AS history_dataset_association_blurb, history_dataset_association.peek AS history_dataset_association_peek, history_dataset_association.tool_version AS history_dataset_association_tool_version, history_dataset_association.extension AS history_dataset_association_extension, history_dataset_association.metadata AS history_dataset_association_metadata, history_dataset_association.parent_id AS history_dataset_association_parent_id, history_dataset_association.designation AS history_dataset_association_designation, history_dataset_association.deleted AS history_dataset_association_deleted, history_dataset_association.purged AS history_dataset_association_purged, history_dataset_association.visible AS history_dataset_association_visible, history_dataset_association.hidden_beneath_collection_instance_id AS history_dataset_association_hidden_beneath_collection_ins_3, history_dataset_association.extended_metadata_id AS history_dataset_association_extended_metadata_id, dataset_1.id AS dataset_1_id, dataset_1.create_time AS dataset_1_create_time, dataset_1.update_time AS dataset_1_update_time, dataset_1.state AS dataset_1_state, dataset_1.deleted AS dataset_1_deleted, dataset_1.purged AS dataset_1_purged, dataset_1.purgable AS dataset_1_purgable, dataset_1.object_store_id AS dataset_1_object_store_id, dataset_1.external_filename AS dataset_1_external_filename, dataset_1._extra_files_path AS dataset_1__extra_files_path, dataset_1.file_size AS dataset_1_file_size, dataset_1.total_size AS dataset_1_total_size, dataset_1.uuid AS dataset_1_uuid FROM history_dataset_association LEFT OUTER JOIN dataset AS dataset_1 ON dataset_1.id = history_dataset_association.dataset_id WHERE history_dataset_association.id = ‘49b19822485c7897' looks like a simple bug to me. But I don’t know an easy way to track it down. Any ideas? Brad -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist

3 6

can't install numpy from toolshed
by Sajdak, Doris 12 Aug '14

12 Aug '14

I'm running Galaxy in a virtual environment as described here (OS is Debian 3.2.54-2): https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Us… When I go to install package_numpy_1_7 from the tool shed, I get the following errors: Running from numpy source directory. /ifs/projects/galaxy/database/tmp/tmp-toolshed-mtdaP2Rhs/numpy-1.7.1/numpy/distutils/command/config.py:413: DeprecationWarning: +++++++++++++++++++++++++++++++++++++++++++++++++ Usage of get_output is deprecated: please do not use it anymore, and avoid configuration checks involving running executable on the target machine. +++++++++++++++++++++++++++++++++++++++++++++++++ DeprecationWarning) Traceback (most recent call last): File "setup.py", line 214, in <module> setup_package() File "setup.py", line 207, in setup_package configuration=configuration ) File "/ifs/projects/galaxy/database/tmp/tmp-toolshed-mtdaP2Rhs/numpy-1.7.1/numpy/distutils/core.py", line 186, in setup return old_setup(**new_attr) File "/usr/lib/python2.6/distutils/core.py", line 152, in setup dist.run_commands() File "/usr/lib/python2.6/distutils/dist.py", line 975, in run_commands self.run_command(cmd) File "/usr/lib/python2.6/distutils/dist.py", line 995, in run_command cmd_obj.run() File "/ifs/projects/galaxy/database/tmp/tmp-toolshed-mtdaP2Rhs/numpy-1.7.1/numpy/distutils/command/install.py", line 55, in run r = old_install.run(self) File "/usr/lib/python2.6/distutils/command/install.py", line 615, in run self.run_command('build') File "/usr/lib/python2.6/distutils/cmd.py", line 333, in run_command self.distribution.run_command(command) File "/usr/lib/python2.6/distutils/dist.py", line 995, in run_command cmd_obj.run() File "/ifs/projects/galaxy/database/tmp/tmp-toolshed-mtdaP2Rhs/numpy-1.7.1/numpy/distutils/command/build.py", line 37, in run old_build.run(self) File "/usr/lib/python2.6/distutils/command/build.py", line 135, in run self.run_command(cmd_name) File "/usr/lib/python2.6/distutils/cmd.py", line 333, in run_command self.distribution.run_command(command) File "/usr/lib/python2.6/distutils/dist.py", line 995, in run_command cmd_obj.run() File "/ifs/projects/galaxy/database/tmp/tmp-toolshed-mtdaP2Rhs/numpy-1.7.1/numpy/distutils/command/build_src.py", line 152, in run self.build_sources() File "/ifs/projects/galaxy/database/tmp/tmp-toolshed-mtdaP2Rhs/numpy-1.7.1/numpy/distutils/command/build_src.py", line 169, in build_sources self.build_extension_sources(ext) File "/ifs/projects/galaxy/database/tmp/tmp-toolshed-mtdaP2Rhs/numpy-1.7.1/numpy/distutils/command/build_src.py", line 328, in build_extension_sources sources = self.generate_sources(sources, ext) File "/ifs/projects/galaxy/database/tmp/tmp-toolshed-mtdaP2Rhs/numpy-1.7.1/numpy/distutils/command/build_src.py", line 385, in generate_sources source = func(extension, build_dir) File "numpy/core/setup.py", line 410, in generate_config_h moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir) File "numpy/core/setup.py", line 41, in check_types out = check_types(*a, **kw) File "numpy/core/setup.py", line 271, in check_types "Cannot compile 'Python.h'. Perhaps you need to "\ SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel. python-dev is installed on the machine, though I don't know if that matters in the virtual environment. Any idea what's causing this? THANKS! Dori ********************************** Dori Sajdak Senior Systems Administrator State University of NY at Buffalo Center for Computational Research 701 Ellicott St Buffalo, NY 14203 Phone: (716) 881-8934 Fax: (716) 849-6656 Web: http://ccr.buffalo.edu **********************************

2 3

Re: [galaxy-dev] Galaxy error
by John Chilton 12 Aug '14

12 Aug '14

Hello, Sorry for the delay - please keep all correspondences on galaxy-dev to maximize the likelihood someone will respond and respond promptly. I do not know what would cause this error - does anyone else have any ideas? -John On Mon, Aug 4, 2014 at 2:07 PM, Beck, Emily A <emily-beck(a)uiowa.edu> wrote: > Sorry for my delayed response. The error is on the main public server, > and happens when I try to map with Bowtie for Illumina. Thank you. > > ~Emily > > > > > *Emily Beck *PhD Candidate > Llopart Lab > 469 Biology Building > Iowa City, IA 52242 > Lab: (319)335-3430 > ------------------------------ > *From:* John Chilton [jmchilton(a)gmail.com] > *Sent:* Tuesday, July 22, 2014 4:06 PM > *To:* Beck, Emily A > *Cc:* galaxy-dev(a)bx.psu.edu > *Subject:* Re: [galaxy-dev] Galaxy error > > Hello, > > Thanks for the bug report. Is this on the main public server ( > usegalaxy.org) or a local instance at the University of Iowa? > > -John > > > On Wed, Jul 16, 2014 at 10:39 AM, Beck, Emily A <emily-beck(a)uiowa.edu> > wrote: > >> >> Hello, >> >> I have repeatedly gotten the following error message when attempting to >> use both the mapping and pileup functions in Galaxy. I am using files that >> I have previously used successfully with these functions, and cannot fix it. >> >> Thank you. >> >> ~Emily Beck >> >> >> user username emilybeck quota_percent 19 total_disk_usage 52086193970 >> nice_total_disk_usage 48.5 GB email emily-beck(a)uiowa.edu is_admin false >> tags_used model_class User id 03f0554e2314759e source >> HDACollection(f313d1d65c4ee57e,451) xhr readyState 4 responseText {"err_msg": >> "Uncaught exception in exposed API method:", "err_code": 0} responseJSON >> err_msg Uncaught exception in exposed API method: err_code 0 status >> 500 statusText Internal Server Error responseHeaders Server nginx/1.4.7 >> Date Wed, 16 Jul 2014 15:19:52 GMT Content-Type application/json >> Transfer-Encoding chunked Connection keep-alive Cache-Control max-age=0,no-cache,no-store >> options data parse true emulateHTTP false emulateJSON false >> >> >> >> *Emily Beck *PhD Candidate >> Llopart Lab >> 469 Biology Building >> Iowa City, IA 52242 >> Lab: (319)335-3430 >> >> ___________________________________________________________ >> 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/ >> > >

2 1

Bug report: <page> within <help>
by Hans-Philipp Brachvogel 12 Aug '14

12 Aug '14

Hello, I found that it is possible for tool-xmls defined with <page> tags to also have multipage helps, but this feature is not really documented and also does not work because of a tiny bug. You can have multipage helps by writing something like this (if your tool has two <page>s): <help> <page> Helptext for page 1 </page> <page> Helptext for page 2 </page> </help> But for it to work one has to fix the following: rev 13771:7a4d321c0e38 file lib/galaxy/tools/__init__.py expression starting at line 1439: self.help_by_page = [ Template( rst_to_html( help_header + x + help_footer, input_encoding='utf-8', output_encoding='utf-8', default_filters=[ 'decode.utf8' ], encoding_errors='replace' ) ) for x in self.help_by_page ] The bracket is misplaced and the whole thing should instead be: self.help_by_page = [ Template( rst_to_html( help_header + x + help_footer), input_encoding='utf-8', output_encoding='utf-8', default_filters=[ 'decode.utf8' ], encoding_errors='replace' ) for x in self.help_by_page ] One question: <page> is deprecated, does this mean there will be no multipage tools in the future? Or will there be (or is already?) an alternative system? Best, Philipp

3 3

TypeError with 'dict'
by Martin Christiansen 12 Aug '14

12 Aug '14

Hi all, I'm setting up a local galaxy server and have implemented a tool, but I can't even get it to run. When I try to run it, the terminal says: TypeError: unhashable type: 'dict' The error itself arises from a python egg: File "~/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/identity.py", line 141 in get state = dict.get(self, key, default) Any suggestions of how to solve this? Best regards, Martin Christiansen

2 2

sql server timeout
by Shrum, Donald C 08 Aug '14

08 Aug '14

On occasion I'm getting and 'Internal Server error' on login with my production galaxy server. If I refresh the page I'm able to login just fine. This instance of galaxy has an apache frontend and a mysql server on the back end. If I look at my log files I see: OperationalError: (OperationalError) (2006, 'MySQL server has gone away') 'SELECT galaxy_session.id AS galaxy_session_id............. It looks like perhaps galaxy is trying to use a stale session or something like that. Has anyone else seen this problem and is there an easy solution aside from having users refresh the page? Thanks, Don FSU Research Computing Center

2 1

ToolShed error: samtools installation failure
by Beginner TI 07 Aug '14

07 Aug '14

2 5

"The status is being set to Never installed"
by David Hoover 07 Aug '14

07 Aug '14

When I install a tool from the toolshed that has type="set_environment" as a requirement, I get this in the main.log: Creating a new record for version None of tool dependency SCRIPT_PATH for revision 5fed38c7e063 of repository mirdeep2. The status is being set to Never installed. Consequently, nothing in the tool_dependency directory is created. The tool is shown to have missing dependencies in the 'Manage installed tool shed repositories' panel. Is there something special that must be done to allow a tool to have only an environment setting as a dependency? Is there something that can be done to fix the problem, other than going into the database and changing the tool_dependency.status from 'Never installed' to 'Installed' and manually creating the subdirectories? -------------------- David Hoover, PhD Helix Systems Staff

1 0

changes to upload.py
by Sajdak, Doris 07 Aug '14

07 Aug '14

I'm in an odd situation: I was given an older version of Galaxy with additional tools built into it by a new faculty member. He brought this from his former institutions and wanted us to run his Galaxy instance on our systems. We don't want to support several instances so we agreed to put his tools into our Galaxy implementation. However, we are running into all kinds of snags. The latest issue is that we realized changes have been made to upload.py to allow for additional data types. Here's an example of what I mean: def check_bam( temp_name ): return Bam().sniff( temp_name ) def check_sff( temp_name ): return Sff().sniff( temp_name ) def check_celstgz( temp_name ): return CelsTgz().sniff( temp_name ) While this doesn't seem like a big deal to add those changes into our installation, I'm concerned that doing so will make us unable to update Galaxy in the future. Can you either confirm or deny that changes to upload.py on our system will be overwritten with Galaxy updates? Thanks, Dori ********************************** Dori Sajdak Senior Systems Administrator State University of NY at Buffalo Center for Computational Research 701 Ellicott St Buffalo, NY 14203 Phone: (716) 881-8934 Fax: (716) 849-6656 Web: http://ccr.buffalo.edu **********************************

2 2