PathoFact issueshttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues2020-04-21T15:09:05+02:00https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/17spring-clean: DeepVirFinder2020-04-21T15:09:05+02:00Valentina Galatavalentina.galata@uni.luspring-clean: DeepVirFinderDependency: `DeepVirFinder`
* [x] `git submodule` (for version see below)
* [x] rm dir. in `scripts/`
* [x] rm `git clone` from `set-up.sh`
* [x] update path in `config.yaml`
```shell
git submodule add https://github.com/jessieren/Deep...Dependency: `DeepVirFinder`
* [x] `git submodule` (for version see below)
* [x] rm dir. in `scripts/`
* [x] rm `git clone` from `set-up.sh`
* [x] update path in `config.yaml`
```shell
git submodule add https://github.com/jessieren/DeepVirFinder.git submodules/DeepVirFinder
cd submodules/DeepVirFinder
git checkout ddb4a94
```
Impact: Could affect the results if there are any discrepancies between the versions of any dependency. Therefore:
- Confirm `git` version
- Use same YAML as in original repospring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/26spring-clean: snakemake rules indentation2020-04-21T14:08:28+02:00Valentina Galatavalentina.galata@uni.luspring-clean: snakemake rules indentationFix formatting in all `snakemake` files (do **NOT** change the commands)
- Indentation: 4 spaces
Impact: Will not affect the pipelineFix formatting in all `snakemake` files (do **NOT** change the commands)
- Indentation: 4 spaces
Impact: Will not affect the pipelinespring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/25spring-clean: rm `configfile` from snakemake rule files2020-04-21T14:08:06+02:00Valentina Galatavalentina.galata@uni.luspring-clean: rm `configfile` from snakemake rule filesRemove `configfile` in all `snakemake` files except in `Snakemake`.
Otherwise it is impossible to use a custom file to call the pipeline.
Impact: Will not affect the pipelineRemove `configfile` in all `snakemake` files except in `Snakemake`.
Otherwise it is impossible to use a custom file to call the pipeline.
Impact: Will not affect the pipelinespring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/24spring-clean: add workflow parameter2020-04-21T13:47:28+02:00Valentina Galatavalentina.galata@uni.luspring-clean: add workflow parameter* [x] Add `workflow` variable to `config.yaml`
* [x] Adjust `Snakemake`* [x] Add `workflow` variable to `config.yaml`
* [x] Adjust `Snakemake`spring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/16spring-clean: main YAML file2020-04-20T14:18:45+02:00Valentina Galatavalentina.galata@uni.luspring-clean: main YAML fileCreate main `conda` YAML file containing
- `python=3.6.4`
- `snakemake=5.5.4`Create main `conda` YAML file containing
- `python=3.6.4`
- `snakemake=5.5.4`spring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/13spring-clean: add .gitignore2020-04-20T14:04:47+02:00Valentina Galatavalentina.galata@uni.luspring-clean: add .gitignore* [x] add `.gitignore`
Impact: Will not affect the pipeline* [x] add `.gitignore`
Impact: Will not affect the pipelinespring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/14spring-clean: mv conda_environments and YAML files2020-04-20T13:46:18+02:00Valentina Galatavalentina.galata@uni.luspring-clean: mv conda_environments and YAML files* [x] mv `conda_environments/` to `envs/` - shorter and more convenient
* [x] mv YAML files: name based on tool, `*.yaml`
* [x] adjust paths in scripts
Impact: Will not affect the pipeline* [x] mv `conda_environments/` to `envs/` - shorter and more convenient
* [x] mv YAML files: name based on tool, `*.yaml`
* [x] adjust paths in scripts
Impact: Will not affect the pipelinespring-cleanValentina 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.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/2PathoFact for metagenome assembled genomes (MAGs)2020-04-14T09:13:30+02:00Christiane HassenrückPathoFact for metagenome assembled genomes (MAGs)Hi @laura.denies
I am quite new to the analysis of virulence factors and antimicrobial resistance genes, and I have been looking for a suitable tool to search for these genes also in MAGs. Your tool looks very promising. If I understoo...Hi @laura.denies
I am quite new to the analysis of virulence factors and antimicrobial resistance genes, and I have been looking for a suitable tool to search for these genes also in MAGs. Your tool looks very promising. If I understood your approach correctly, PathoFact takes as input the assembly (i.e. contigs) and the predicted ORF before the binning step. Would it also be possible to run PathoFact on the binned genomes (MAGs)? Would the performance of the tool be reduced by having less complex input (i.e. MAGs instead of the full metagenome assembly)?
Thanks a lot for your advise!
Kind regards,
Christianehttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/1Missing file2020-02-03T10:30:44+01:00Susheel BusiMissing fileHi,
Thanks for a great tool. I tried running it this morning, but a file seems to be missing! See error message below:
`cannot access scripts/VirSorter/wrapper_phage_contigs_sorter_iPlant.pl: No such file or directory`
-SusheelHi,
Thanks for a great tool. I tried running it this morning, but a file seems to be missing! See error message below:
`cannot access scripts/VirSorter/wrapper_phage_contigs_sorter_iPlant.pl: No such file or directory`
-SusheelLaura DeniesLaura Denies