snakemake-tutorial | head node of an HPC cluster running Slurm

 by   nathanhaigh Python Version: Current License: No License

kandi X-RAY | snakemake-tutorial Summary

kandi X-RAY | snakemake-tutorial Summary

snakemake-tutorial is a Python library. snakemake-tutorial has no bugs, it has no vulnerabilities and it has low support. However snakemake-tutorial build file is not available. You can download it from GitHub.

For the purpose of the webinar we will be working on the head node of an HPC cluster running Slurm. This is the most likely infrastructure that fellow bioinformaticians already find themselves using on a regular basis. The execution of the Snakemake workflow will actually take place on the cluster head node with jobs being submitted to Slurm for queing and processing. From the head node, Snakemake will monitor the submitted jobs for their completion status and submit new jobs as dependent jobs complete sucessfully.
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              snakemake-tutorial has a low active ecosystem.
              It has 4 star(s) with 3 fork(s). There are 1 watchers for this library.
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              It had no major release in the last 6 months.
              snakemake-tutorial has no issues reported. There are 1 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of snakemake-tutorial is current.

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              snakemake-tutorial has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

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              snakemake-tutorial releases are not available. You will need to build from source code and install.
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              Installation instructions, examples and code snippets are available.

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            snakemake-tutorial Key Features

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            snakemake-tutorial Examples and Code Snippets

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            Community Discussions

            QUESTION

            Snakemake: how to use one integer from list each call as input to script?
            Asked 2020-Oct-28 at 08:52

            I'm trying to practice writing workflows in snakemake.

            The contents of my Snakefile:

            ...

            ANSWER

            Answered 2020-Oct-28 at 08:52

            Looks like you want to run your Rscript twice per file, once for every value of col. In this case, the rule needs to be called twice as well. The use of expand is also a bit too much here, in my opinion. expand fills your wildcards with all possible values and returns a list of the resulting files. So the output for this rule would be all possible combinations between files and cols, which the simple script can not create in one run. This is also the reason why file can not be inferred from the output - it gets expanded there.

            Instead, try writing your rule easier for just one file and column and expand on the resulting output, in a rule which needs this output as an input. If you generated the final output of your workflow, put it as input in a rule all to tell the workflow what the ultimate goal is.

            Source https://stackoverflow.com/questions/64566297

            QUESTION

            Execute a Snakemake workflow via Tibanna on AWS
            Asked 2020-Sep-10 at 12:37

            I am trying to execute the workflow of the Snakemake's official tutorial via Tibanna on AWS.

            As instructed here,

            1. I have installed Tibanna and set up environment variables.
            2. Then I deployed Tibanna Unicorn to a folder snakemake-tutorial in a specific S3 bucket specific-bucket.
            3. I set up the default unicorn.
            4. As a last step, I run the following command:
            ...

            ANSWER

            Answered 2020-Sep-10 at 12:37

            I was able to solve this problem with the --precommand flag.

            Source https://stackoverflow.com/questions/63778054

            QUESTION

            What are the conditions for snakemake to execute a job?
            Asked 2020-Jun-17 at 03:51

            I would like to know all necessary criteria required for snakemake to decide that a job needs to be executed, but I couldn't find them in their documentation. The best source I have found is in snakemake author's slides from 2016, which says:

            ...

            ANSWER

            Answered 2020-Jun-17 at 03:51

            This page of their documentation has a link to the slides from 2019: https://snakemake.readthedocs.io/en/stable/tutorial/tutorial.html. On the page 26 of the slides you may see the same set of rules: https://slides.com/johanneskoester/snakemake-tutorial#/25:

            Source https://stackoverflow.com/questions/62419042

            QUESTION

            Snakemake - Problem trying to use global_wildcards (TypeError: expected str, got list)
            Asked 2020-Mar-12 at 15:53

            I'm a newbie using Snakemake and not an expert in Python neither so the answer might be quite obvious. Everything in my workflow worked fine in my tests until I tried to use glob_wildcards in order to turn all of my fastq.gz files from one directory (FASTQDIR) into fastqc files.

            The samples names in the SAMPLES list are okay but I have an error saying that a string is expected instead of a list (I assume this is my SAMPLES list) and I don't really know where to act in my Snakefile in order to correct it. I understand that it is surely linked to my use of glob_wildcards but I don't understand where is the problem. Do you have an idea of how I can fix it ?

            Here is my Snakefile code :

            ...

            ANSWER

            Answered 2020-Mar-12 at 15:53

            You are not using wildcards here.

            Your rule fastqc_generate_qc takes as input ALL the fastq files and output ALL the fastqc files here.
            One thing to remember in snakemake is: expand produces a list of files. You don't want that here:

            Source https://stackoverflow.com/questions/60526646

            QUESTION

            snakemake substitution issue
            Asked 2019-Jul-12 at 17:44

            I am new to snakemake and have an issue with the following code that should take 9 fastq files one after another and apply fastqc.

            smp should take the values:

            UG1_S12 UG2_S13 UG3_S14 UR1_S1 UR2_S2 UR3_S3 UY1_S6 UY2_S7 UY3_S8

            Which works when I run

            ...

            ANSWER

            Answered 2018-Oct-24 at 15:21

            If you want to use the wildcards in the shell command, you have to use {wildcards.smp} .
            What is probably happening is that {smp} in the shell command takes the value of the last iteration of the for loop above. So change:

            Source https://stackoverflow.com/questions/52967024

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            Vulnerabilities

            No vulnerabilities reported

            Install snakemake-tutorial

            The recommended installation route for Snakemake is through a conda environemnt. As such, you need Anaconda3, usually avaiable to you on your cluster via the module system.

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