wBuild issueshttps://gitlab.cmm.in.tum.de/wachutka/wBuild/-/issues2018-01-24T16:35:57Zhttps://gitlab.cmm.in.tum.de/wachutka/wBuild/-/issues/3add wbuild demo2018-01-24T16:35:57ZLeonhard Wachutkaadd wbuild demo- [x] define variables outside report.R
- where? maybe in `make.config` or `.Rprofile`
- use them in i) the wbuild header of report.R
- and ii) in the R-code
- [x] define variables in wbuild header and use them in R-code, e.g. t...- [x] define variables outside report.R
- where? maybe in `make.config` or `.Rprofile`
- use them in i) the wbuild header of report.R
- and ii) in the R-code
- [x] define variables in wbuild header and use them in R-code, e.g. this [makeData.R](https://i12g-gagneurweb.informatik.tu-muenchen.de/gitlab/wachutka/wBuild/blob/master/wbuild/demo/Scripts/Task1/makeData.R)
- [x] compile a single script file with wBuild (to use the variables from the header); best without defining a rule in `Snakefile`
## Tasks for the sprint
- [ ] choose an example dataset to use throughout the demo
- go through the whole tutorial
- Pages
- [x] simple input page
- single input file, plot the results (iris dataset)
- [x] input-output page
- script parameters (choose whether it should be rendered or not)
- one script does PCA
- second one plots it
- [x] plain snakefiles inclusion - show how to do this
- show how to download the iris dataset if it doesnt exist
- say that if you would have removed the file, everything else would still run
- [x] describe how the markdown inclusion works
- [x] How to use plain python in the header using escape sequences
- case-study: apply one script multiple times using wildcards
- run model on three different columns, save all the models to the output
- [ ] softlinking/scriptMapping the analysis scripts automatically
- show how to apply the same pipeline to 2 different datasets (have two scripts)
- for the second one, modify the plot file
- [ ] show the commands implemented in snakemake and also supported by wbuild
- DAG
- all
- publish
- explain the config file
- script-mapping
- [ ] adapt the process of getting the dataset for windows
- `wget` is a command unique for Linux and doesn't launch on Windows
- skip wgetting the dataset and instead ship it already bundled in demo?Hackaton #1Leonhard WachutkaLeonhard Wachutkahttps://gitlab.cmm.in.tum.de/wachutka/wBuild/-/issues/61Cheatsheet of wbuild commands2019-12-18T18:57:40ZLuise SchullerCheatsheet of wbuild commandsIt would be so nice to have a cheatsheet with wbuild commands, header etc. The demos are helping but only at the beginning. Afterwards, it would be so nice to get to known further commands, things etc. wbuild is capable of.It would be so nice to have a cheatsheet with wbuild commands, header etc. The demos are helping but only at the beginning. Afterwards, it would be so nice to get to known further commands, things etc. wbuild is capable of.https://gitlab.cmm.in.tum.de/wachutka/wBuild/-/issues/60Updating wbuild demo (Example 050_PythonCode)2019-12-18T18:55:21ZLuise SchullerUpdating wbuild demo (Example 050_PythonCode)In wbuild demo (Demoset 050_PythonCode) it seems like, that id.txt is created within the script 020_CreateIDs.R. But with a closure look it is delivered in Data and not created by 020_CreateIDs.R. 020_CreateIDs.R is even not build with ...In wbuild demo (Demoset 050_PythonCode) it seems like, that id.txt is created within the script 020_CreateIDs.R. But with a closure look it is delivered in Data and not created by 020_CreateIDs.R. 020_CreateIDs.R is even not build with we build with wbuild. It would be better to either delete the script 020_CreateIDs.R or fix it, that it will create the id.txt which will be used by the 040_IndexIDs.R script.https://gitlab.cmm.in.tum.de/wachutka/wBuild/-/issues/59working with different configs2019-06-25T10:07:01ZMichaela Müllerworking with different configsCurrently it is required to put configuration information into a file specifically named `wbuild.yaml` in the repo root. It is an issue with snakemake, that it's difficult to get the config file name that was passed in the command line i...Currently it is required to put configuration information into a file specifically named `wbuild.yaml` in the repo root. It is an issue with snakemake, that it's difficult to get the config file name that was passed in the command line into the Snakefile.Michaela MüllerMichaela Müllerhttps://gitlab.cmm.in.tum.de/wachutka/wBuild/-/issues/58Wbuild init and update overwriting2019-06-25T10:03:28ZMichaela MüllerWbuild init and update overwritingIt would be more convenient for `wbuild init` and `wbuild update` not to overwrite already existing README, Snakefile, and config files.It would be more convenient for `wbuild init` and `wbuild update` not to overwrite already existing README, Snakefile, and config files.https://gitlab.cmm.in.tum.de/wachutka/wBuild/-/issues/57Rulegraph instead of job graph2019-06-25T10:01:27ZMichaela MüllerRulegraph instead of job graphI propose to replace the jobgraph (annoying, if you have to run 100 files) with a rulegraph (as provided by snakemake) instead. This is a lot easier to read.I propose to replace the jobgraph (annoying, if you have to run 100 files) with a rulegraph (as provided by snakemake) instead. This is a lot easier to read.Michaela MüllerMichaela Müllerhttps://gitlab.cmm.in.tum.de/wachutka/wBuild/-/issues/56Include header template in the documentation?2018-05-26T05:36:10ZStefan DvoretskiiInclude header template in the documentation?I've noticed that through all the time that I use wBuild I pretty much use the same code template, including
```
source('.wBuild/wBuildParser.R')
parseWBHeader("Scripts/SNPplot/Main/calcMean.R")
```
which was not that apparent at the ...I've noticed that through all the time that I use wBuild I pretty much use the same code template, including
```
source('.wBuild/wBuildParser.R')
parseWBHeader("Scripts/SNPplot/Main/calcMean.R")
```
which was not that apparent at the beginning.https://gitlab.cmm.in.tum.de/wachutka/wBuild/-/issues/55Testing2018-05-12T22:21:18ZStefan DvoretskiiTestingWe could improve the quality of software a lot testing it
- [ ] improve cli.py tests
- [ ] test where possibleWe could improve the quality of software a lot testing it
- [ ] improve cli.py tests
- [ ] test where possiblehttps://gitlab.cmm.in.tum.de/wachutka/wBuild/-/issues/54Search report pages2018-05-09T14:47:09ZStefan DvoretskiiSearch report pagesFind and integrate some open source library to allow users searching through the rendered HTML report.Find and integrate some open source library to allow users searching through the rendered HTML report.https://gitlab.cmm.in.tum.de/wachutka/wBuild/-/issues/52Demo (report pages) documentation: structure & contents2018-05-09T14:01:06ZStefan DvoretskiiDemo (report pages) documentation: structure & contents[ ] rename tabs?
[ ] add table of contents to the main site (potentially buggy) ?[ ] rename tabs?
[ ] add table of contents to the main site (potentially buggy) ?https://gitlab.cmm.in.tum.de/wachutka/wBuild/-/issues/46HTML output: make tab title appropriate2018-03-06T11:19:22ZGhost UserHTML output: make tab title appropriateWhen one opens the HTML files, there is just a tab name 'title' to see. We could enter something more describing and appropriate there, so that's possible for users to identify that that's the wbuild output.
Screenshot attached:![2018-0...When one opens the HTML files, there is just a tab name 'title' to see. We could enter something more describing and appropriate there, so that's possible for users to identify that that's the wbuild output.
Screenshot attached:![2018-02-28_18_19_58-title](/uploads/6188d672f8f90ab4f755c6c8de2a700a/2018-02-28_18_19_58-title.png)https://gitlab.cmm.in.tum.de/wachutka/wBuild/-/issues/36Web render issues2018-05-09T12:40:28ZGhost UserWeb render issues- [ ] - customizing - layout, menu structure etc.
- [ ] - `javascript('navigate')` blocks opening link in a new tab- [ ] - customizing - layout, menu structure etc.
- [ ] - `javascript('navigate')` blocks opening link in a new tabhttps://gitlab.cmm.in.tum.de/wachutka/wBuild/-/issues/35Python binding2018-02-02T13:28:43ZGhost UserPython bindingAllow parsing headers/rendering of the py filesAllow parsing headers/rendering of the py fileshttps://gitlab.cmm.in.tum.de/wachutka/wBuild/-/issues/33R-Py binding2018-02-02T13:20:51ZGhost UserR-Py bindingDecouple parsing headers from snakemake to allow it to be launced from R function via vanilla Python binding. Snakemake (could) provide a rule here that would return the snakemake object to the R code for the later work with it.Decouple parsing headers from snakemake to allow it to be launced from R function via vanilla Python binding. Snakemake (could) provide a rule here that would return the snakemake object to the R code for the later work with it.https://gitlab.cmm.in.tum.de/wachutka/wBuild/-/issues/25Make all the paths to files raw2018-02-02T12:58:46ZGhost UserMake all the paths to files rawI've e.g. put the directory in "C:\Users\...", which presumably a lot of users will also do, and got an error for using \U escape character.
We have to determine all the places where paths are being used by OS and make them raw strings.I've e.g. put the directory in "C:\Users\...", which presumably a lot of users will also do, and got an error for using \U escape character.
We have to determine all the places where paths are being used by OS and make them raw strings.https://gitlab.cmm.in.tum.de/wachutka/wBuild/-/issues/20Script mapping2018-02-02T12:21:21ZLeonhard WachutkaScript mapping- [ ] - Windows issues
- [ ] - Documentation
- [ ] - Merging with wBuild.yaml- [ ] - Windows issues
- [ ] - Documentation
- [ ] - Merging with wBuild.yamlhttps://gitlab.cmm.in.tum.de/wachutka/wBuild/-/issues/12Save snakemake object for debuging2017-10-27T18:42:38ZChristian MertesSave snakemake object for debugingIf you experience problems with your script it would be nice if you could debug it with the snakemake object given by the pipeline.
Is it possible to save the snakemake object in a tmp folder by default? this would make debuging much ea...If you experience problems with your script it would be nice if you could debug it with the snakemake object given by the pipeline.
Is it possible to save the snakemake object in a tmp folder by default? this would make debuging much easier. Of course you could save it in your own script each time, but I think it would make it easier if you just save it by default in a tmp folder.
What do you think about it @wachutka @ravindrs?Leonhard WachutkaLeonhard Wachutkahttps://gitlab.cmm.in.tum.de/wachutka/wBuild/-/issues/7wbuild init witout any example files2018-02-28T13:46:47ZChristian Merteswbuild init witout any example filesIf you run `wbuild init` it creates a default folder structure.
This is nice if you never worked with wbuild. But if you have already a full working structure and you just want to get wbuild to work you do not need them. It would be nic...If you run `wbuild init` it creates a default folder structure.
This is nice if you never worked with wbuild. But if you have already a full working structure and you just want to get wbuild to work you do not need them. It would be nice to have a option where you could suppress the creation of the example files.
Also it overrides the Snakemake file which should not be the case. Especially if you have already some customised rules in it.
This is a follow up of the issue: baderda/sample_annotation#12
@wachutka and @baderda could be interested too.https://gitlab.cmm.in.tum.de/wachutka/wBuild/-/issues/6table of content2017-09-11T08:20:44ZDaniel Magnus Badertable of content- [ ] Could we have the floating toc on the left side, since wide tables extend to the right, possible into the TOC.
- [ ] Can we make the TOC wider than default knitr, say 150px, 200px?
- [ ] There is much white space between "recent f...- [ ] Could we have the floating toc on the left side, since wide tables extend to the right, possible into the TOC.
- [ ] Can we make the TOC wider than default knitr, say 150px, 200px?
- [ ] There is much white space between "recent files" and the main text of the page, we could use it.
Happy to hear your opinion @wachutka