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galaxyproject / tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission
https://galaxyproject.org/iuc
MIT License
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HiC Tools on Main #398

Closed nekrut closed 7 years ago

nekrut commented 8 years ago

To deploy Hi-C tools on main:

bgruening commented 7 years ago

@jxtx any new about HiFive? We are close for a TS release for HiCExplorer + IE.

jxtx commented 7 years ago

@msauria What's preventing hifive from being in the ToolShed? It has a conda package so dependencies are easily handled now.

martenson commented 7 years ago

@jxtx some version (2/11/16) of hifive is on toolshed: https://toolshed.g2.bx.psu.edu/view/sauria/hifive/20dfaec1678c

jxtx commented 7 years ago

Right, my understanding was something prevented this from being deployed to main but I don't know what.

jxtx commented 7 years ago

@msauria update the hifive tools to use conda for dependencies and we tested the install last week. He is planning to add more tests by I don't think we should wait for that. This is ready to go to main @martenson. Can we create an "NGS: Chromosome Conformation" section with these tools in it and a "HiFive" section label, any other tools can go in this section with their own label.

martenson commented 7 years ago

Will do.

On Mon, Jan 16, 2017, 11:15 James Taylor notifications@github.com wrote:

@msauria https://github.com/msauria update the hifive tools to use conda for dependencies and we tested the install last week. He is planning to add more tests by I don't think we should wait for that. This is ready to go to main @martenson https://github.com/martenson. Can we create an "NGS: Chromosome Conformation" section with these tools in it and a "HiFive" section label, any other tools can go in this section with their own label.

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martenson commented 7 years ago

hifive is on Main now @jxtx @msauria - once cvmfs publishes the thing it should be visible I will adjust the sections and labels tomorrow.

edit: on Main live: https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/sauria/hifive/hifive/0.1.0

jxtx commented 7 years ago

Awesome!

martenson commented 7 years ago

hifive's section now in the right place in toolpanel under a label and with a label

jennaj commented 7 years ago

The link to the tool github repo (for the galaxy wrapped version, not the line-command version) is incorrect in the Tool Shed, and I didn't find it in tools-devteam or tools-iuc, so I am not sure where to put this issue with the wrapper. Please move it to where it would be appropriate.

At Galaxy Main, the wrapper is failing for option -c ("Included chromosomes"). This is under the operation "Create HiC Project". As an aside, if that field is left empty, the tool fails for another reason. Both are below for troubleshooting.

When a chromosome is entered on form, this error:

Command Line

hifive  hic-project   -c chr14   -f 20 -j 1000 -n 100   -m 1000000 -x 0  /galaxy-repl/main/files/018/933/dataset_18933773.dat /galaxy-repl/main/files/018/933/dataset_18933827.dat -q
stderr

Fatal error: Exit code 2 ()
usage: hifive [-h] [--version]
              {fragments,5c-data,5c-project,5c-normalize,5c-complete,5c-heatmap,5c-interval,5c-combine-replicates,fends,hic-data,hic-project,hic-normalize,hic-complete,hic-heatmap,hic-mrheatmap,hic-interval,hic-combine-replicates}
              ...
hifive: error: unrecognized arguments: -c /galaxy-repl/main/files/018/933/dataset_18933827.dat
example:

Job ID  15106165 (bbd44e69cb8906b58a44c5361b6b5a72)
Tool ID toolshed.g2.bx.psu.edu/repos/sauria/hifive/hifive/0.1.0
Tool Version    0.1.0
Job PID or DRM id   9261176.roundup

When no chromosome is entered on form, this error: (should this be required input at job submission?)

Command Line

hifive  hic-project     -f 20 -j 1000 -n 100   -m 1000000 -x 0  /galaxy-repl/main/files/018/933/dataset_18933773.dat /galaxy-repl/main/files/018/944/dataset_18944613.dat -q
stderr

Fatal error: Exit code 1 ()
divide by zero encountered in log
invalid value encountered in multiply
Traceback (most recent call last):
  File "/galaxy/main/deps/_conda/envs/__hifive@1.3/bin/hifive", line 4, in <module>
    __import__('pkg_resources').run_script('hifive==1.3.0', 'hifive')
  File "/galaxy/main/deps/_conda/envs/__hifive@1.3/lib/python2.7/site-packages/pkg_resources/__init__.py", line 739, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/galaxy/main/deps/_conda/envs/__hifive@1.3/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1494, in run_script
    exec(code, namespace, namespace)
  File "/cvmfs/main.galaxyproject.org/deps/_conda/envs/__hifive@1.3/lib/python2.7/site-packages/hifive-1.3.0-py2.7-linux-x86_64.egg-info/scripts/hifive", line 791, in <module>
    main()
  File "/cvmfs/main.galaxyproject.org/deps/_conda/envs/__hifive@1.3/lib/python2.7/site-packages/hifive-1.3.0-py2.7-linux-x86_64.egg-info/scripts/hifive", line 69, in main
    run(args)
  File "/galaxy/main/deps/_conda/envs/__hifive@1.3/lib/python2.7/site-packages/hifive/commands/create_hic_project.py", line 32, in run
    hic.find_distance_parameters(minsize=args.minbin, numbins=args.numbins)
  File "/galaxy/main/deps/_conda/envs/__hifive@1.3/lib/python2.7/site-packages/hifive/hic.py", line 491, in find_distance_parameters
    distance_parameters = numpy.zeros((valid.shape[0] - 1, 3), dtype=numpy.float32)
ValueError: negative dimensions are not allowed
example: 

Job ID  15113738 (bbd44e69cb8906b52b808b92b4de2e28)
Tool ID toolshed.g2.bx.psu.edu/repos/sauria/hifive/hifive/0.1.0
Tool Version    0.1.0
Job PID or DRM id   9268351.roundup
bgruening commented 7 years ago

@jxtx can we move these tools into tools-iuc?

jxtx commented 7 years ago

Up to @msauria

jxtx commented 7 years ago

@bgruening I just talked to @msauria. He is pushing a new version of HiFive to address the issues and he is happy to have the IUC adopt the wrappers.

bgruening commented 7 years ago

Awesome, thanks @msauria and @jxtx!