Re: [galaxy-dev] Error editing users associated with a quota
On Mon, Nov 11, 2013 at 6:55 PM, John Chilton chil...@msi.umn.edu wrote: Hey Peter, Does your universe_wsgi.ini have enable_quotas = True set? -John No, $ grep enable_quotas universe_wsgi.ini (nothing) I had suspected the quotas might not be working... If the default is not to enable quotas, then the Manage quotas entry of the Admin page ought perhaps to be disabled? 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/
[galaxy-dev] dynamic_options selected value as input for second dynamic_options function call
Hello, I would like to have a tool form with a two parameters: 1. Select State 2. Select Town The options for 'Select State' are dynamically generated with dynamic_options which calls a python function, which connects to a database and returns the list of States. This works fine in my form xml code: param name = State_id type=select dynamic_options=getStates() label=Select State display=radio multiple=false Now I want to dynamically create the options for '2. Select Town'. To make this work I need to take the selected option from '1. Select State', pass it as an argument to a dynamic_options function call that would then connect to a database and retrieve the Towns for the provided State. These Towns would then be the options for '2. Select Town'. So, the second parameter '2. Select Town' should do something like this: param name = Town_id type=select dynamic_options=getTowns([user selected value in 1. Select State]) label=Select Town display=radio multiple=false The part in square brackets is pseudo code; this is the part that I cannot get to work . That part should also be automatically refreshed if the user changes the selection in '1. Select State'. I looked into the use of conditional but I don't see how I can use that if I don't know beforehand what values I can have (determined in real time based on content of database), so I cannot code the when tags. Any help is greatly appreciated. Thank you in advance, Hans ___ 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] BAM/BAI index file test problem on (Test) Tool Shed
Hi guys, I have a new wrapper for samtools idxstats with a working unit test via run_functional_tests.sh run locally or on TravisCI: https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-November/017406.html However, this tool's test is failing on the Test Tool Shed: http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats/6564815949e0 Tool test results Automated test environment Time tested: ~ 11 hours ago System: Linux 3.8.0-30-generic Architecture: x86_64 Python version: 2.7.4 Galaxy revision: 11284:28469a503b56 Galaxy database version: 117 Tool shed revision: Tool shed database version: Tool shed mercurial version: Tests that failed Tool id: samtools_idxstats Tool version: samtools_idxstats Test: test_tool_00 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_idxstats/samtools_idxstats/0.0.1) Stderr: Fatal error: Exit code 1 () Input BAI file not found: None Traceback: Traceback (most recent call last): File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 216, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 28, in do_it self.__verify_outputs( testdef, shed_tool_id, data_list ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 134, in __verify_outputs self.__verify_output( output_tuple, shed_tool_id, elem, maxseconds=maxseconds ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 141, in __verify_output self.verify_dataset_correctness( outfile, hid=elem_hid, attributes=attributes, shed_tool_id=shed_tool_id ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py, line 782, in verify_dataset_correctness self._assert_dataset_state( elem, 'ok' ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py, line 606, in _assert_dataset_state raise AssertionError( errmsg ) AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error It appears that the upload has not generated the *.bai index and assigned it to the variable input_bam.metadata.bam_index (but this works via run_functional_tests.sh for me): $ ls test-data/ex1.* test-data/ex1.bam test-data/ex1.idxstats.tabular $ ./run_functional_tests.sh -id samtools_idxstats ... Ran 1 test in 32.400s OK ... (all fine) (Note that the bai file does not seem to be needed) Tested with this revision, which works: $ hg branch default $ hg log | head changeset: 12309:1df960b4892a tag: tip user:John Chilton jmchil...@gmail.com date:Sun Nov 10 23:37:56 2013 -0600 summary: PEP-8 cleanups of lib/galaxy/security/__init__.py. Updated to current tip, also works: $ hg branch default [galaxy@ppserver galaxy-central]$ hg log | head changeset: 12321:e12a10e5418d tag: tip user:guerler date:Mon Nov 11 16:00:10 2013 -0500 summary: UI: Fix tooltip placement for masthead icons Are there anyone known differences on the Test Tool Shed which could explain this failure? Thanks, 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/
Re: [galaxy-dev] BAM/BAI index file test problem on (Test) Tool Shed
This sounds a lot like this; http://dev.list.galaxyproject.org/galaxy-cant-find-binaries-in-tp4662442p4662444.html. When using the local job runner (as the test framework likely does), I believe samtools needs to be on Galaxy's path. I don't think it is enough to just have it available as a tool dependency (installed via tool shed or not). As workarounds Dave could either install the samtools OS package or place the tool shed install of this on Galaxy's path before starting? .Alternatively, I guess the underlying problem could be solved - though it is not entirely clear the best path forward on that, only that is a real problem. -John On Tue, Nov 12, 2013 at 6:07 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi guys, I have a new wrapper for samtools idxstats with a working unit test via run_functional_tests.sh run locally or on TravisCI: https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-November/017406.html However, this tool's test is failing on the Test Tool Shed: http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats/6564815949e0 Tool test results Automated test environment Time tested: ~ 11 hours ago System: Linux 3.8.0-30-generic Architecture: x86_64 Python version: 2.7.4 Galaxy revision: 11284:28469a503b56 Galaxy database version: 117 Tool shed revision: Tool shed database version: Tool shed mercurial version: Tests that failed Tool id: samtools_idxstats Tool version: samtools_idxstats Test: test_tool_00 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_idxstats/samtools_idxstats/0.0.1) Stderr: Fatal error: Exit code 1 () Input BAI file not found: None Traceback: Traceback (most recent call last): File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 216, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 28, in do_it self.__verify_outputs( testdef, shed_tool_id, data_list ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 134, in __verify_outputs self.__verify_output( output_tuple, shed_tool_id, elem, maxseconds=maxseconds ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 141, in __verify_output self.verify_dataset_correctness( outfile, hid=elem_hid, attributes=attributes, shed_tool_id=shed_tool_id ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py, line 782, in verify_dataset_correctness self._assert_dataset_state( elem, 'ok' ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py, line 606, in _assert_dataset_state raise AssertionError( errmsg ) AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error It appears that the upload has not generated the *.bai index and assigned it to the variable input_bam.metadata.bam_index (but this works via run_functional_tests.sh for me): $ ls test-data/ex1.* test-data/ex1.bam test-data/ex1.idxstats.tabular $ ./run_functional_tests.sh -id samtools_idxstats ... Ran 1 test in 32.400s OK ... (all fine) (Note that the bai file does not seem to be needed) Tested with this revision, which works: $ hg branch default $ hg log | head changeset: 12309:1df960b4892a tag: tip user:John Chilton jmchil...@gmail.com date:Sun Nov 10 23:37:56 2013 -0600 summary: PEP-8 cleanups of lib/galaxy/security/__init__.py. Updated to current tip, also works: $ hg branch default [galaxy@ppserver galaxy-central]$ hg log | head changeset: 12321:e12a10e5418d tag: tip user:guerler date:Mon Nov 11 16:00:10 2013 -0500 summary: UI: Fix tooltip placement for masthead icons Are there anyone known differences on the Test Tool Shed which could explain this failure? Thanks, 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
Re: [galaxy-dev] BAM/BAI index file test problem on (Test) Tool Shed
Hello Peter, Thanks for reporting this - I've added the following Trello card for this issue. https://trello.com/c/sN2iLCCn/99-bug-in-install-and-test-framework-1 Greg Von Kuster On Nov 12, 2013, at 7:07 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi guys, I have a new wrapper for samtools idxstats with a working unit test via run_functional_tests.sh run locally or on TravisCI: https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-November/017406.html However, this tool's test is failing on the Test Tool Shed: http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats/6564815949e0 Tool test results Automated test environment Time tested: ~ 11 hours ago System: Linux 3.8.0-30-generic Architecture: x86_64 Python version: 2.7.4 Galaxy revision: 11284:28469a503b56 Galaxy database version: 117 Tool shed revision: Tool shed database version: Tool shed mercurial version: Tests that failed Tool id: samtools_idxstats Tool version: samtools_idxstats Test: test_tool_00 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_idxstats/samtools_idxstats/0.0.1) Stderr: Fatal error: Exit code 1 () Input BAI file not found: None Traceback: Traceback (most recent call last): File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 216, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 28, in do_it self.__verify_outputs( testdef, shed_tool_id, data_list ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 134, in __verify_outputs self.__verify_output( output_tuple, shed_tool_id, elem, maxseconds=maxseconds ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 141, in __verify_output self.verify_dataset_correctness( outfile, hid=elem_hid, attributes=attributes, shed_tool_id=shed_tool_id ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py, line 782, in verify_dataset_correctness self._assert_dataset_state( elem, 'ok' ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py, line 606, in _assert_dataset_state raise AssertionError( errmsg ) AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error It appears that the upload has not generated the *.bai index and assigned it to the variable input_bam.metadata.bam_index (but this works via run_functional_tests.sh for me): $ ls test-data/ex1.* test-data/ex1.bam test-data/ex1.idxstats.tabular $ ./run_functional_tests.sh -id samtools_idxstats ... Ran 1 test in 32.400s OK ... (all fine) (Note that the bai file does not seem to be needed) Tested with this revision, which works: $ hg branch default $ hg log | head changeset: 12309:1df960b4892a tag: tip user:John Chilton jmchil...@gmail.com date:Sun Nov 10 23:37:56 2013 -0600 summary: PEP-8 cleanups of lib/galaxy/security/__init__.py. Updated to current tip, also works: $ hg branch default [galaxy@ppserver galaxy-central]$ hg log | head changeset: 12321:e12a10e5418d tag: tip user:guerler date:Mon Nov 11 16:00:10 2013 -0500 summary: UI: Fix tooltip placement for masthead icons Are there anyone known differences on the Test Tool Shed which could explain this failure? Thanks, 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] BAM/BAI index file test problem on (Test) Tool Shed
On Tue, Nov 12, 2013 at 2:37 PM, John Chilton chil...@msi.umn.edu wrote: This sounds a lot like this; http://dev.list.galaxyproject.org/galaxy-cant-find-binaries-in-tp4662442p4662444.html. When using the local job runner (as the test framework likely does), I believe samtools needs to be on Galaxy's path. I don't think it is enough to just have it available as a tool dependency (installed via tool shed or not). As workarounds Dave could either install the samtools OS package or place the tool shed install of this on Galaxy's path before starting? .Alternatively, I guess the underlying problem could be solved - though it is not entirely clear the best path forward on that, only that is a real problem. -John Yes, that sounds like the same problem - and I agree a short term hack would be to put samtools on the test system. On Tue, Nov 12, 2013 at 2:35 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Peter, Thanks for reporting this - I've added the following Trello card for this issue. https://trello.com/c/sN2iLCCn/99-bug-in-install-and-test-framework-1 Greg Von Kuster That Trello link seems to be broken for me :( 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/
Re: [galaxy-dev] Error editing users associated with a quota
On Tue, Nov 12, 2013 at 3:32 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, Nov 11, 2013 at 6:55 PM, John Chilton chil...@msi.umn.edu wrote: Hey Peter, Does your universe_wsgi.ini have enable_quotas = True set? -John No, $ grep enable_quotas universe_wsgi.ini (nothing) I had suspected the quotas might not be working... If the default is not to enable quotas, then the Manage quotas entry of the Admin page ought perhaps to be disabled? I was going to make you Trello card for this entirely logical request and then I decided in the time it would take the Trello interface to load I could do a pull request instead. https://bitbucket.org/galaxy/galaxy-central/pull-request/258/only-show-manage-quotas-if-quotas-are/diff 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/
Re: [galaxy-dev] Error editing users associated with a quota
On Tue, Nov 12, 2013 at 3:12 PM, John Chilton chil...@msi.umn.edu wrote: On Tue, Nov 12, 2013 at 3:32 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, Nov 11, 2013 at 6:55 PM, John Chilton chil...@msi.umn.edu wrote: Hey Peter, Does your universe_wsgi.ini have enable_quotas = True set? -John No, $ grep enable_quotas universe_wsgi.ini (nothing) I had suspected the quotas might not be working... If the default is not to enable quotas, then the Manage quotas entry of the Admin page ought perhaps to be disabled? I was going to make you Trello card for this entirely logical request and then I decided in the time it would take the Trello interface to load I could do a pull request instead. https://bitbucket.org/galaxy/galaxy-central/pull-request/258/only-show-manage-quotas-if-quotas-are/diff Thanks - at some point I will need to set enable_quotas = True, and retest to see if the original bug persists. 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/
[galaxy-dev] Write all intermediate workflow data to /tmp/ only
I'm working with a lot of data on a cluster (condor). If I save all the workflow intermediate data, as Galaxy does by default (and rightfully so), it fills the drives. How can tell Galaxy to use /tmp/ to store all intermediate data in a workflow, and keep the result? I imagine I'll have to work on how Galaxy handles jobs, but I'm hoping there is something built in for this. Thanks ___ 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_options selected value as input for second dynamic_options function call
Hi, I found a working workaround using the deprecated page tags: inputs page param name = State_id type=select dynamic_options=getStates() label=Select State display=radio multiple=false/ /page page param name = Town_id type=select dynamic_options=getTowns(State_id) label=Select Town display=radio multiple=false/ /page /inputs This works; both select lists (on separate GUI pages) are dynamically generated when the called function connects to a database to retrieve the options. However, as it is recommended not to use page tags any longer, can anyone suggest how to write above example using condition and when tags instead? I have searched a lot but can't find out how to do it. Thank you, Hans ___ 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 Lindsay, Nice to hear that Vipin's server worked out for you. A reduction in the number of lines is completely expected. You should have the same number of lines in the BED12 file as you have unique IDs in the GFF3 file, if you want to double check. This is the same as the number of unique transcripts in any of the files, if summed up correctly. Why is this? A GFF3 file has one line per feature. Part of an exon, etc. with further (this can vary) annotation that tells you if it is 5' UTR, or CDS, etc. When converting GFF3 - BED12, all the features for a particular transcript are rolled up into a single line of output. Transcripts will have a unique ID by GFF3 specification - and all features that belong to that transcript will have it in the GFF3 file's attributes field (it is usually the first attribute listed). When you converted just GFF3 - BED6, each feature was individually converted into a distinct line of BED formatted output, there was no summing up to group the information for the transcript as a whole. The Galaxy wiki has more - GFF3 can represent other kinds of data, and that is covered in the link-outs to the original spec, but this is the gist of the meaning for your specific data. Glad I could help before, and that Vipin had the tool online available to simplify things! Best, Jen Galaxy team On 11/12/13 4:12 PM, Lindsay Rutter wrote: Hello Jennifer: Thank you for your very helpful and detailed explanation! I ended up using the site that Vipin provided in his message (https://galaxy.cbio.mskcc.org/tool_runner?tool_id=fml_gff2bed). Indeed, it produced a file with 12 columns that appears to be in a reasonable bed format (including the 10th column being an integer, with the 11th and 12th column consisting of that integer number of items separated by commas). However, I noticed that the number of lines in the file went from 183,748 (in the .gff3 file) to 11,506 (in the 12-column .bed file). In your opinion, does this seem like a reasonable reduction in number of lines? I was not expecting that (in fact, I was expecting the number of lines would stay the same, as they did going from .gff3 to 6-column .bed file), but I am quite inexperienced using these files. Thanking you... Lindsay On Mon, Nov 11, 2013 at 11:15 AM, Jennifer Jackson j...@bx.psu.edu mailto: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 http://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 http://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 http://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.
