ShouWenWang
commented
2 weeks ago It is often needed to install pear on a HPC locally so that no root permission is needed. To do so, you can use ./configure --prefix /local/directory to install it locally where you do have access. Below is an example script for installing pear on HPC locally.
cd pear_installation_folder
./configure --prefix ~ # install at the local home directory
make
make installThe warning.txt file is not showing up because we modified the MatLab code. I don’t think this is that useful. You will need to inspect the output Results.txt file yourself to get how this could be wrong. Some of the guidelines for trouble shooting:
@.***
From: jzussman @.> Date: Friday, July 5, 2024 at 8:18 AM To: ShouWenWang-Lab/snakemake_DARLIN @.> Cc: Subscribed @.***> Subject: [ShouWenWang-Lab/snakemake_DARLIN] Running on HPC without sudo privileges -- PEAR install? FastQC/MultiQC Issues (Issue #10)
Hello, I've been working with CARLIN data using the prior MATLAB pipeline and was very excited to migrate to this improved snakemake_DARLIN implementation for batch submissions. I would like to run the snakemake_DARLIN pipeline on an HPC with MATLAB available but have been unable to install PEAR properly without sudo privileges -- do you have a recommended install method? Alternatively, I noticed that the python version of the pipeline does not seem to require a pear installation, is this true?
In addition, while running snakemake_DARLIN locally I was hoping to receive the Warnings.txt file in addition to the other outputs. Does this require fastqc/multiqc? I installed both to the snakemake_DARLIN conda environment but still did not receive a Warnings.txt file when running snakemake_DARLIN. How should fastqc and multiqc be installed in order to get the requisite QC info?
— Reply to this email directly, view it on GitHubhttps://github.com/ShouWenWang-Lab/snakemake_DARLIN/issues/10, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABDCASXCJS3IH6ETMPSMOILZKXQ6JAVCNFSM6AAAAABKMIFXQKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGM4TCNJXGIZTCNI. You are receiving this because you are subscribed to this thread.Message ID: @.***>
jzussman
Hello, I've been working with CARLIN data using the prior MATLAB pipeline and was very excited to migrate to this improved snakemake_DARLIN implementation for batch submissions. I would like to run the snakemake_DARLIN pipeline on an HPC with MATLAB available but PEAR installation has been tricky; is it sufficient to have PEAR installed into the conda environment via bioconda? Alternatively, I noticed that the python version of the pipeline does not seem to require a pear installation, is this true?
In addition, while running snakemake_DARLIN locally I was hoping to receive the Warnings.txt file in addition to the other outputs. Does this require fastqc/multiqc? I installed both to the snakemake_DARLIN conda environment but still did not receive a Warnings.txt file when running snakemake_DARLIN. How should fastqc and multiqc be installed in order to get the requisite QC info?