Problem installing the rna-seq-pop

[dieunelderilus]

Hi rna-seq-pop developper,

I am having problem installing this pipeline using conda: ls config LICENSE README.md resources RNA-Seq-Pop-Logo.png workflow

snakemake --use-conda --cores 16 _WorkflowErrorin line 13 of /scicomp/home-pure/qlk5/Desktop/important_programs/rna-seq-pop/workflow/Snakefile: Workflow defines configfile config/config.yaml but it is not present or accessible. File "/scicomp/home-pure/qlk5/Desktop/importantprograms/rna-seq-pop/workflow/Snakefile", line 13, in

It looks like we need a file called config.yaml inside of the config folder , which is not exists , see bellow: ls ../rna-seq-pop/o_config/ exampleconfig.yaml examplefastq.tsv examplesamples.tsv __ Please, do you have any suggestion?

Cheers, DD

[sanjaynagi]

Hello there @dieunelderilus !

RNA-Seq-Pop does indeed need a 'config.yaml' file. You should rename the 'exampleconfig.yaml' file in the config/ folder, and edit the workflow options in the config.yaml file to choose which bits of analysis you would like to run.

I apologise for the lack of the documentation. In the next few days, I will make a quick video walkthrough of how to set up the workflow and set it running on some data. Let me know if/when you run into issues, and ill be on hand to help.

[sanjaynagi]

As an aside Dieunel - it would be really cool for you to re-analyse your arabiensis data from Ethiopia with the workflow! :)

[dieunelderilus]

Hi @sanjaynagi, Thank you for your quick response. Yes, the documentation is missing. What about it copy .test/config/ folder to the root folder of the repository and run the workflow as you have suggested? I try to do that and get some thing like that: snakemake --use-conda --cores 16 _---------------------------- RNA-Seq-Pop ---------------------------- Running RNA-Seq-Pop snakemake workflow in /scicomp/home-pure/qlk5/Desktop/important_programs/rna-seq-pop/workflow

Author: Sanjay Curtis Nagi Workflow Version: v1.0.1 Execution time: 2022-09-30 16:16:04.089342 Dataset: Test-TravisCI

Migrating .snakemake folder to new format... Migration complete Building DAG of jobs... MissingInputException in rule KallistoIndex in line 2 of /scicomp/home-pure/qlk5/Desktop/important_programs/rna-seq-pop/workflow/rules/alignment.smk: Missing input files for rule KallistoIndex: output: resources/reference/kallisto.idx affected files: resources/reference/Anopheles-gambiae-PEST_TRANSCRIPTSAgamP4.12-X.fa Do you think that the installation was successful?

Yes , I am currently running a comparative RNA-seq analysis of An funestus, and I want to use the RNA-pop and compare the results. I really like the component of population transcriptomic analysis from your pipeline. Cheers, ~DD

Cheers, ~DD

[sanjaynagi]

To clarify - when you are running these commands, you are not installing the workflow, but running the workflow itself. Strictly speaking, there is no installation needed, apart from having snakemake and conda installed, and the workflow will install any dependencies if you use --use-conda, as you are already.

And no, you should not copy the config folder from the .test folder, this is set up differently, and just to run the test data set. Instead, do as I described above. If you want to run the test dataset to check everything is working correctly, you could run from the rna-seq-pop root directory.

snakemake --use-conda --directory .test/ --cores n

[dieunelderilus]

Thank you so much for this clarification! I will go ahead and run the test data.

[sanjaynagi]

Hi @dieunelderilus , just to say some docs are now written at https://sanjaynagi.github.io/rna-seq-pop/landing-page.html , I will be making a video in the near future.