PathoFact issueshttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues2020-02-03T10:30:44+01:00https://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 Denieshttps://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/3DeepARG -- git lsf issue2021-01-12T15:24:52+01:00Valentina Galatavalentina.galata@uni.luDeepARG -- git lsf issueThe issue is described [here](https://bitbucket.org/gusphdproj/deeparg-ss/issues/1/git-lfs-erros-when-cloning-the-repository).
It seems to have no effect on tool execution.The issue is described [here](https://bitbucket.org/gusphdproj/deeparg-ss/issues/1/git-lfs-erros-when-cloning-the-repository).
It seems to have no effect on tool execution.Paper review - Microbiome - 1https://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/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/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/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/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/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/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/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/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/15spring-clean: all scripts in scripts/2020-04-23T12:31:27+02:00Valentina Galatavalentina.galata@uni.luspring-clean: all scripts in scripts/* [x] mv scripts in `rules/` to `scripts/`
* [x] adjust paths when calling these scripts
Impact: Will not affect the pipeline* [x] mv scripts in `rules/` to `scripts/`
* [x] adjust paths when calling these scripts
Impact: Will not affect the pipelinespring-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/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/18spring-clean: give snakemake files an extension2020-04-24T10:43:37+02:00Valentina Galatavalentina.galata@uni.luspring-clean: give snakemake files an extensionAdd `.smk` to all `snakemake` files in `rules/` and `workflows/`.
Makes it easier to recognize `snakemake` files and to have code highlighting in editors.Add `.smk` to all `snakemake` files in `rules/` and `workflows/`.
Makes it easier to recognize `snakemake` files and to have code highlighting in editors.spring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/19spring-clean: DeepARG2020-04-21T15:09:05+02:00Valentina Galatavalentina.galata@uni.luspring-clean: DeepARGDependency: `DeepARG`
* [x] `git submodule`
* [x] rm dir. in `scripts/`
* [x] rm `git clone` from `set-up.sh`
* [x] update path in `config.yaml`
* [x] set-up commands: replace path and make `DIAMOND` bin executable
```shell
git lfs ins...Dependency: `DeepARG`
* [x] `git submodule`
* [x] rm dir. in `scripts/`
* [x] rm `git clone` from `set-up.sh`
* [x] update path in `config.yaml`
* [x] set-up commands: replace path and make `DIAMOND` bin executable
```shell
git lfs install # if not already done
git submodule add https://gaarangoa@bitbucket.org/gusphdproj/deeparg-ss.git submodules/deeparg-ss
cd submodules/deeparg-ss/
git checkout 14b8dce
```
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/20spring-clean: PlasFlow2020-04-21T15:09:05+02:00Valentina Galatavalentina.galata@uni.luspring-clean: PlasFlowDependency: `PlasFlow`
* [x] `conda` YAML file
* [x] rm dir. in `scripts/`
* [x] update path in `config.yaml`
* [x] add YAML to rule(s) calling `PlasFlow`
Impact: Could affect the results if there are any discrepancies between the versi...Dependency: `PlasFlow`
* [x] `conda` YAML file
* [x] rm dir. in `scripts/`
* [x] update path in `config.yaml`
* [x] add YAML to rule(s) calling `PlasFlow`
Impact: Could affect the results if there are any discrepancies between the versions of any dependency.
Using `conda` installation (`plasflow=1.1.0`) instead of `git` repo (commit `v1.1-11-g82e9c75`).
**NOTE**: [release v1.1 vs. v1.1-11-g82e9c75](https://github.com/smaegol/PlasFlow/compare/v1.1...v1.1-11-g82e9c75)
- README update
- changed description of arg parser in `PlasFlow.py`
- no other changes in the code
--> No critical changesspring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/21spring-clean: VirSorter2020-04-21T15:10:53+02:00Valentina Galatavalentina.galata@uni.luspring-clean: VirSorterDependency: `VirSorter`
* [x] `conda` YAML file
* [x] rm dir. in `scripts/`
* [x] rm `git clone` from `set-up.sh`
* [x] update path in `config.yaml`
Impact: Could affect the results if there are any discrepancies between the versions o...Dependency: `VirSorter`
* [x] `conda` YAML file
* [x] rm dir. in `scripts/`
* [x] rm `git clone` from `set-up.sh`
* [x] update path in `config.yaml`
Impact: Could affect the results if there are any discrepancies between the versions of any dependency.
Using `conda` installation (XX) instead of `git` repo (commit `v1.0.6-2-g52a1cd6`).
**NOTE**: [v1.0.6 vs. v1.0.6-2-g52a1cd6](https://github.com/simroux/VirSorter/compare/v1.0.6...v1.0.6-2-g52a1cd6)
--> **not sure** if all changes are non-criticalspring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.lu