Commit 9542b334 authored by Christian Arnold's avatar Christian Arnold

Improved macOS compatibility for download script

parent 20d26c31
......@@ -3,19 +3,22 @@
Try it out now!
============================================================
The following quick start briefly summarizes the necessary steps to use our pipeline:
diffTF runs on Linux and macOS. The following quick start briefly summarizes the necessary steps to use our pipeline:
1. Install the necessary tools (*Snakemake*, *samtools*, *bedtools*, and *Subread*).
.. note:: Note that all tools require Python 3.
We recommend installing them via conda, in which case the installation is as easy as
We recommend installing them via conda, in which case the installation then becomes as easy as
.. code-block:: Bash
conda install -c bioconda snakemake bedtools samtools subread
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
conda install snakemake bedtools samtools subread
If conda is not yet installed, follow the `installation instructions <https://conda.io/docs/user-guide/install/index.html>`_. Installation is quick and easy.
If conda is not yet installed, follow the `installation instructions <https://conda.io/docs/user-guide/install/index.html>`_. Installation is quick and easy. Make sure to open a new terminal after installation, so that *conda* is available.
.. note:: You do not need to uninstall other Python installations or packages in order to use conda. Even if you already have a system Python, another Python installation from a source such as the macOS Homebrew package manager and globally installed packages from pip such as pandas and NumPy, you do not need to uninstall, remove, or change any of them before using conda.
......
......@@ -373,7 +373,7 @@ It must contain at least contain the following columns (the exact names do matte
- if applicable, all additional variables from the design formula except ``conditionSummary`` must also be present as a separate column.
.. warning:: Do not change the samples data after you started an analysis. You may introduce inconsistencies that will result in error messages. If you need to alter the sample data, we strongly advise to recalculate all steps in the pipeline.
.. warning:: Do not change the samples data after you started an analysis. You may introduce inconsistencies that will result in error messages. If you need to alter the sample data, we strongly advise to recalculate all steps in the pipeline.
Output
************************************************************
......@@ -841,9 +841,10 @@ Identify the cause
To troubleshoot errors, you have to first locate the exact error. Depending on how you run Snakemake (i.e., in a cluster setting or not), check the following places:
- in locale mode: the Snakemake output on the console. Errors from R script should also be written to the corresponding R log files in the in the ``LOGS_AND_BENCHMARKS`` directory.
- in locale mode: the Snakemake output appears on the console. Check the output before the line "Error in rule", and try to identify what went wrong. Errors from R script should in addition be written to the corresponding R log files in the in the ``LOGS_AND_BENCHMARKS`` directory.
- in cluster mode: either error, output or log file of the corresponding rule that threw the error in the ``LOGS_AND_BENCHMARKS`` directory. If you are unsure in which file to look, identify the rule name that caused the error and search for files that contain the rule name in it
Fixing the error
==============================
......
......@@ -2,10 +2,10 @@
# Simply execute with "sh downloadAllData.sh"
filename="exampleData.tar.gz"
wget -O $filename https://www.embl.de/download/zaugg/diffTF/$filename && tar xvzf $filename --overwrite && rm $filename
curl -0 https://www.embl.de/download/zaugg/diffTF/$filename -o $filename && tar xvzf $filename && rm $filename
filename="mm10.fa.tar.gz"
wget -O $filename https://www.embl.de/download/zaugg/diffTF/referenceGenome/$filename && mkdir referenceGenome && tar xvzf $filename -C referenceGenome --overwrite && rm $filename
curl -0 $filename https://www.embl.de/download/zaugg/diffTF/referenceGenome/$filename -o $filename && mkdir referenceGenome && tar xvzf $filename -C referenceGenome && rm $filename
filename="TFBS_mm10_PWMScan_HOCOMOCOv10.tar.gz"
wget -O $filename https://www.embl.de/download/zaugg/diffTF/TFBS/$filename && tar xvzf $filename --overwrite && rm $filename
curl -0 $filename https://www.embl.de/download/zaugg/diffTF/TFBS/$filename -o $filename && tar xvzf $filename && rm $filename
SampleID Condition bamReads Peaks conditionSummary
GMP.WT.1 GMP /g/scb2/zaugg/carnold/Projects/diffTF/example/input/data/bam/GMP.WT.1.chr1.bam /g/scb2/zaugg/carnold/Projects/diffTF/example/input/data/peaks/GMP.WT.1.narrowPeak GMP
GMP.WT.2 GMP /g/scb2/zaugg/carnold/Projects/diffTF/example/input/data/bam/GMP.WT.2.chr1.bam /g/scb2/zaugg/carnold/Projects/diffTF/example/input/data/peaks/GMP.WT.2.narrowPeak GMP
GMP.WT.3 GMP /g/scb2/zaugg/carnold/Projects/diffTF/example/input/data/bam/GMP.WT.3.chr1.bam /g/scb2/zaugg/carnold/Projects/diffTF/example/input/data/peaks/GMP.WT.3.narrowPeak GMP
GMP.WT.4 GMP /g/scb2/zaugg/carnold/Projects/diffTF/example/input/data/bam/GMP.WT.4.chr1.bam /g/scb2/zaugg/carnold/Projects/diffTF/example/input/data/peaks/GMP.WT.4.narrowPeak GMP
MPP.WT.1 MPP /g/scb2/zaugg/carnold/Projects/diffTF/example/input/data/bam/MPP.WT.1.chr1.bam /g/scb2/zaugg/carnold/Projects/diffTF/example/input/data/peaks/MPP.WT.1.narrowPeak MPP
MPP.WT.2 MPP /g/scb2/zaugg/carnold/Projects/diffTF/example/input/data/bam/MPP.WT.2.chr1.bam /g/scb2/zaugg/carnold/Projects/diffTF/example/input/data/peaks/MPP.WT.2.narrowPeak MPP
MPP.WT.3 MPP /g/scb2/zaugg/carnold/Projects/diffTF/example/input/data/bam/MPP.WT.3.chr1.bam /g/scb2/zaugg/carnold/Projects/diffTF/example/input/data/peaks/MPP.WT.3.narrowPeak MPP
MPP.WT.4 MPP /g/scb2/zaugg/carnold/Projects/diffTF/example/input/data/bam/MPP.WT.4.chr1.bam /g/scb2/zaugg/carnold/Projects/diffTF/example/input/data/peaks/MPP.WT.4.narrowPeak MPP
GMP.WT.1 GMP data/bam/GMP.WT.1.chr1.bam data/peaks/GMP.WT.1.narrowPeak GMP
GMP.WT.2 GMP data/bam/GMP.WT.2.chr1.bam data/peaks/GMP.WT.2.narrowPeak GMP
GMP.WT.3 GMP data/bam/GMP.WT.3.chr1.bam data/peaks/GMP.WT.3.narrowPeak GMP
GMP.WT.4 GMP data/bam/GMP.WT.4.chr1.bam data/peaks/GMP.WT.4.narrowPeak GMP
MPP.WT.1 MPP data/bam/MPP.WT.1.chr1.bam data/peaks/MPP.WT.1.narrowPeak MPP
MPP.WT.2 MPP data/bam/MPP.WT.2.chr1.bam data/peaks/MPP.WT.2.narrowPeak MPP
MPP.WT.3 MPP data/bam/MPP.WT.3.chr1.bam data/peaks/MPP.WT.3.narrowPeak MPP
MPP.WT.4 MPP data/bam/MPP.WT.4.chr1.bam data/peaks/MPP.WT.4.narrowPeak MPP
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