PathoFact issueshttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues2020-05-05T07:19:17+02:00https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/7IMPiris: log files2020-05-05T07:19:17+02:00Valentina Galatavalentina.galata@uni.luIMPiris: log filesAdd `log` files to rules
* [x] redirect for CMD
* [ ] logging in scripts
* [x] R scripts
* [ ] Python scriptsAdd `log` files to rules
* [x] redirect for CMD
* [ ] logging in scripts
* [x] R scripts
* [ ] Python scriptsValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/9IMPiris: test data2020-05-05T07:19:06+02:00Valentina Galatavalentina.galata@uni.luIMPiris: test dataCreate a test data setCreate a test data setValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/4IMPiris: new conda dependencies2020-04-17T12:46:47+02:00Valentina Galatavalentina.galata@uni.luIMPiris: new conda dependenciesCreate `conda` YAML files for:
* [x] `hmmer`, version `3.2.1`, [conda](https://anaconda.org/bioconda/hmmer)
* [x] `plasflow`, version `1.1.0`, [conda](https://anaconda.org/smaegol/plasflow)
* [x] `virsorter`, version `1.0.5`, [conda](ht...Create `conda` YAML files for:
* [x] `hmmer`, version `3.2.1`, [conda](https://anaconda.org/bioconda/hmmer)
* [x] `plasflow`, version `1.1.0`, [conda](https://anaconda.org/smaegol/plasflow)
* [x] `virsorter`, version `1.0.5`, [conda](https://anaconda.org/bioconda/virsorter)
* [x] dep.s for `deeparg` using `pip`: [readme](https://bitbucket.org/gusphdproj/deeparg-ss/src/master/), [nolearn dep.s](https://raw.githubusercontent.com/dnouri/nolearn/0.6.0/requirements.txt)
- numpy==1.10.4
- scipy==0.16.1
- Theano==0.8
- -e git+https://github.com/Lasagne/Lasagne.git@8f4f9b2#egg=Lasagne==0.2.git
- joblib==0.9.3
- scikit-learn==0.17
- tabulate==0.7.5
- nolearn==0.6.0
- tqdmValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/12IMPiris: mv all scripts to scripts/2020-04-17T11:29:57+02:00Valentina Galatavalentina.galata@uni.luIMPiris: mv all scripts to scripts/Valentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/11IMPiris: logging in R-scripts2020-04-17T11:29:51+02:00Valentina Galatavalentina.galata@uni.luIMPiris: logging in R-scriptsAdd logging to R-scripts
```R
# Logging
sink(file=file(snakemake@log[[1]], open="wt"), type="message")
```Add logging to R-scripts
```R
# Logging
sink(file=file(snakemake@log[[1]], open="wt"), type="message")
```Valentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/8IMPiris: modify rule messages2020-04-17T11:29:46+02:00Valentina Galatavalentina.galata@uni.luIMPiris: modify rule messages- Every rule should have a message
- It should be clear from the text which rule is executed- Every rule should have a message
- It should be clear from the text which rule is executedValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/6IMPiris: escape tabs in rule CMDs2020-04-17T11:29:41+02:00Valentina Galatavalentina.galata@uni.luIMPiris: escape tabs in rule CMDsEscape `\t` properly by using `\\t` s.t. `snakemake` does not interpret themEscape `\t` properly by using `\\t` s.t. `snakemake` does not interpret themValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/5IMPiris: Add workflow option to config2020-04-17T11:29:30+02:00Valentina Galatavalentina.galata@uni.luIMPiris: Add workflow option to configAdd `workflow` to `config.yaml` and change/replace variable `w` in main `snakemake` fileAdd `workflow` to `config.yaml` and change/replace variable `w` in main `snakemake` fileValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.lu