[x] Do you use the latest HiCExplorer release? If not, please install it via a conda environment:
conda create --name hicexplorer hicexplorer=3.6 python=3.8 -c bioconda -c conda-forge
and activate the environment: conda activate hicexplorer. Retry your command. You can exit a conda environment via conda deactivate. To learn more about conda and environments, please consider the following documentation.
Retry your command, is it solved now? If not please continue with the following:
[x] Paste the full HiCExplorer command that produces the issue below
(ignore if you simply spotted the issue in the code/documentation).
[x] Paste the output printed on screen from the command that produces the issue
below (ignore if you simply spotted the issue in the code/documentation).
I am implementing a hic-explorer pipeline in WDL via cromwell for deployment in AWS.
One of the easiest ways to reduce running time, in pipelines is usually to chop up fastq-files (scatter), run the entire pipeline with each chunk, and then merge the results (gather). If I do this with the hic-explorer pipeline, can I run hicSumMatrices across all the matrices generated for each chunk and get an equivalent matrix as if I run the whole pipeline with one pair of big fastq files?
Welcome to the HiCExplorer GitHub repository! Before opening the issue please check that the following requirements are met :
[x] Search whether this issue (or a similar issue) has been solved before using the search tab above. Link the previous issue if appropriate below.
[x] Paste your HiCExplorer version (
hicInfo --version) and your python version (python --version) below. 3.7.2[x] Have you checked our documentation on hicexplorer.readthedocs.io?
[x] Do you use conda to install HiCExplorer?
[x] Do you use the latest HiCExplorer release? If not, please install it via a conda environment:
conda create --name hicexplorer hicexplorer=3.6 python=3.8 -c bioconda -c conda-forgeand activate the environment:conda activate hicexplorer. Retry your command. You can exit a conda environment viaconda deactivate. To learn more about conda and environments, please consider the following documentation.Retry your command, is it solved now? If not please continue with the following:
[x] Paste the full HiCExplorer command that produces the issue below (ignore if you simply spotted the issue in the code/documentation).
[x] Paste the output printed on screen from the command that produces the issue below (ignore if you simply spotted the issue in the code/documentation).
I am implementing a hic-explorer pipeline in WDL via cromwell for deployment in AWS. One of the easiest ways to reduce running time, in pipelines is usually to chop up fastq-files (scatter), run the entire pipeline with each chunk, and then merge the results (gather). If I do this with the hic-explorer pipeline, can I run
hicSumMatricesacross all the matrices generated for each chunk and get an equivalent matrix as if I run the whole pipeline with one pair of big fastq files?