lmrodriguezr / enveomics-gui Goto Github PK
View Code? Open in Web Editor NEWGraphical User Interface of the Enveomics collection
Home Page: http://enve-omics.ce.gatech.edu/enveomics/gui
License: Artistic License 2.0
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Log file for recent runs
Auto install crashes on enveomics.R
Issue migrated from lmrodriguezr/enveomics#19 @cpadilla7:
Hello,
Whenever I try to run auto install enveomics.r auto install from the GUI the program stalls then crashes, any suggestions?
Thanks!
Mac OS X apps have low resolution
Check it out:
This is probably associated with the retina-enabled versions, but it needs further investigation. The problem appears to arise during bundleing, because opening the jar directly with java -jar -XstartOnFirstThread dist/enveomics.jar solves this problem:
List top-5 most frequently used scripts at "/home"
This will require the creation of configuration files within ~/.enveomics.
Citations needed
Script-specific citations should be added. Add support for a references field in manifest.json.
Manual or help
For example:
Each program needs some documentation as to what and how to get the input files. For example, Blast output from NCBI website is not necessarily identical to the stand-alone version. At the very least, the pdf file with short description should be accessable through the interface.
Enveomics crashes when opened and says "retrieving enveomics" after terminal installation
Hi, I'm new to programming but have been working on metagenomics using our lab server. I'm trying to install enveomics on my windows 10 and have installed ruby and perl. My script shows the io/console error but it seems to run. When I open Enveomics, it stays on a frozen screen saying "retrieving enveomics" and it either crashes when I click on a tab or just crashes by it self. Any suggestions?
optparse R library should be included
Auto-check for updates
Perhaps on start-up? Maybe the GitHub API could be used for this.
We need Search option
Categories are handy, but sometimes direct searching is much more convenient, we need a search option.
Support R functions
Probably this needs some work over at https://github.com/lmrodriguez/enveomics, to create RScripts that are directly accessible from CLI.
jar file uses commands from an older version of java that do not work with the current version
Hello
I am having trouble downloading the enveomics GUI onto my Windows PC. It seems like the jar file uses commands from an older version of java that do not work with the current version of the package loader I am using (openJDK). Do you have any advice on how to fix this? Or do you recommend another package?
Thanks in advance
Laura
Unmet requirements even when the system has them
There are some reports of the GUI complaining about unmet requirements even after installing them. This was reported for the R package enveomics.R. Information on the issue is scarce, but it's most likely caused by a mismatch between the R in which the package was installed and the R being used by the GUI.
NameError: missing class or uppercase package name (`org.eclipse.swt.widgets.Text')
Hi,
I downloaded enveomics.jar and tried to open it with java -jar enveomics.jar but got the error in the attached file.
stdout.txt
I'm using Ubuntu 20.04 and jruby --version gives me:
jruby 9.1.17.0 (2.3.3) 2020-02-29 fffffff OpenJDK 64-Bit Server VM 11.0.11+9-Ubuntu-0ubuntu2.20.04 on 11.0.11+9-Ubuntu-0ubuntu2.20.04 +jit [linux-x86_64]
Do you know what the problem might be?
Thanks a lot!
Matthias
Pipelines broken in Ubuntu
When running a task in Ubuntu, the stdout is lost and the stderr is sent directly to the console, nothing is saved in the temporal file. I suspect this might be due to the OS-specific implementation of Open3.start_pipeline, used for tasks execution. Currently, a single command is passed, including stderr and stdout redirection. Probably a better approach would be for EnveTask to return an array (instead of a single string), to be passed as arguments to Open3.start_pipeline with a splat (*). The outputs then become problematic, since many scripts use stdout and/or stderr to save output files (which are declared as options), but this might be an option. Perhaps an even better way to deal with this would be to include the Open3 call in EnveTask, and return the wait_thr instead of the command. The problem would be that the reported command would have to be simulated, but that shouldn't be a problem.
Kill processes
The children processes are detached, which means that there is no way to terminate a process from within the GUI (not even closing the GUI). It would be nice to have a "kill" button in the running window, but it would also be desirable to kill processes when closing the running window.
:multiple_sep silently ignored
The :multiple_sep key of manifest.json options is silently ignored. It should, instead, allow for multiple values.
Important: manifest.json currently uses this key only with " " values for input files, but it should be implemented in a general manner. The value should be passed unescaped (so " " allows for multiple arguments, but "\ " allows for a single argument of space-delimited entries). Other common value would be ",", which is commonly used in ruby scripts to split an argument into array entries, and is common for arguments other than :in_file.
Support manifest.json :see_also
Enable support once lmrodriguezr/enveomics#9 is solved.
Support manifest.json :suggests
Needs a back button
It needs a “Back” button to go to the originating category rather than going back home and clicking your way back into the category.
bundled app not working on OS X 10.6.8
$ ./enveomics.app/Contents/MacOS/JavaAppLauncher
Thu Dec 10 16:48:07 est3321-ktk3-05.ce.gatech.edu JavaAppLauncher[69983] <Error>: kCGErrorInvalidConnection: CGSGetCurrentCursorLocation: Invalid connection
Thu Dec 10 16:48:07 est3321-ktk3-05.ce.gatech.edu JavaAppLauncher[69983] <Error>: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged.However, the jar works perfectly.
Some defaults ignored silently
The defaults for check (:nil) and lists (:select) are not being taken into account. Checks should never default to true, otherwise they would be, by definition, not the default. However, lists are defaulting to no-selection, even though many explicitly set defaults.
Mac OS X apps don't load full environment
For some reason the bundled apps are not loading the full environment, perhaps they're not sourcing ~/.profile? This is a big issue, because it means incompatibility with package managers like brew.
The environment is successfully inherited when called from the command line (with either of /Applications/enveomics.app/Contents/MacOS/JavaAppLauncher or open /Applications/enveomics.app), just not when opened on double-click.
Halting v0.1.0 release until this is solved.
CLI animations are noisy in run outputs
Some scripts use \r to simulate animations (e.g., for advance bars), but the GUI simply takes them as new lines, producing a rather noisy output. For example, what should be a clean:
Objective minimum distance: 0.3755282, initial tips: 110
| Iter: 0, Tips: 110, Median distance: 1.979233, Minimum distance: 6.152532e-06
|======================================================================| 100%
| Iter: 1, Tips: 69, Median distance: 2.071625, Minimum distance: 9.228798e-06
|======================================================================| 100%
| Iter: 2, Tips: 50, Median distance: 2.237375, Minimum distance: 9.228798e-06
|======================================================================| 100%
| Iter: 3, Tips: 43, Median distance: 2.359235, Minimum distance: 0.2096652
|======================================================================| 100%
| Iter: 4, Tips: 41, Median distance: 2.394462, Minimum distance: 0.4001159
Is shown as:
Objective minimum distance: 0.3755282, initial tips: 110
Gathering distances...
| Iter: 0, Tips: 110, Median distance: 1.979233, Minimum distance: 6.152532e-06
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Gathering distances...
| Iter: 1, Tips: 69, Median distance: 2.071625, Minimum distance: 9.228798e-06
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Gathering distances...
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Gathering distances...
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Gathering distances...
| Iter: 4, Tips: 41, Median distance: 2.394462, Minimum distance: 0.4001159
I'll sneak this in v0.1.0-rc3, since it's an easy fix and I have to solve #22 before the release.
EnveCollection HOME in OS X
It's currently set to ~/.enveomics, but it would be more appropriate to set it to ~/Library/enveomics.
Ruby 2 should be shipped
1/3 of the scripts use Ruby, and most of them require Ruby 2+, which is not the default for most systems (in OS X it only became the default one release ago). In addition, many scripts require a few of gems (like Nokogiri) that would be better to include in the bundles. The most appealing solution seems to be Traveling Ruby.
Ruby minimum version not tested
Most (all?) Ruby scripts in the collection require ruby >= 2.0.0, but lower versions silently pass all tests and result in cryptic syntax errors (e.g., for syntax {key: "value"} was previously not supported). This should be considered when addressing #7.
:source_url silently ignored
Options have a :source_url field that should be rendered as a link.
Poor rendering of top icons in Ubuntu
Probably due to the rescaling of the icons from 500x500 down to 50x50. I should scale it down once and ship them with the app. Check it out:
Also, I should reduce the font size for the icon titles in Linux (or increase the inner-most stack), so "All tasks" doesn't get split in two lines.
:warn in tasks
Some tasks need a :warn key, for example for deprecated scripts.
Improve unzip master.zip in EnveGUI::home
This code doesn't look very safe. At the very least I should double-check that it works in all distros, but it most likely won't (e.g., Win).
In-app examples
Support for an :example key for tasks in manifest.json (see lmrodriguezr/enveomics#14)
This has been requested to conform with editorial requirements, so I've got to rush it into the first release.
Allow hiding non-mandatory options
A button toggling non-mandatory options display would be very handy.
BLAST binaries won't work in linux 32bit
Only 64bit binaries are shipped, and a cryptic error is returned on failure. I should include 32bit binaries and test for architecture if OS Linux.
Failed installations break the GUI
The failure is captured but the alert breaks the GUI
Users should be able to control interpreters
The interpreters used (see EnveTask class-level section) are guesses for the best available option, but users should be allowed to modify these values if necessary.
Auto-include :requires per language
Include checks for languages (perl, ruby, bash, etc) based on task suffixes.
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