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Hopefully by now you have had enough experience installing packages via conda that it is second nature to think of going to https://anaconda.org/ searching for multiqc, finding https://anaconda.org/bioconda/multiqc, and seeing that it recommends a command of conda install -c bioconda multiqc suggesting you can use this command and not worry about anything else. Instead, if you go to the multiqc homepage you might (or might probably not, disappointingly, it is not very visible disappointingly) that next to their conda installation instruction is a small warning icon which takes you to a page about setting up bioconda channels as a prerequisite to installing multiqc. Friday's class will go into detail about managing channels like this and it is not suggested that you follow the commands on that page.
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| Line number | As is | To be |
|---|---|---|
| 16 | #SBATCH -J jobName | #SBATCH -J multiqc |
| 17 | #SBATCH -n 1 | #SBATCH -n 6848 |
| 21 | #SBATCH -t 12:00:00 | #SBATCH -t 0:20:00 |
| 22 | ##SBATCH --mail-user=ADD | #SBATCH --mail-user=<YourEmailAddress> |
| 23 | ##SBATCH --mail-type=all | #SBATCH --mail-type=all |
| 29 | export LAUNCHER_JOB_FILE=commands | export LAUNCHER_JOB_FILE=breseq_commands |
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| Code Block | ||||
|---|---|---|---|---|
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fastqc -t 6848 -o fastqc_output/ *.gz |
Using both the * wildcard, and 68 48 threads, analysis of many samples are initiated at the same time making the output somewhat difficult to read, but significantly increasing the speed at which the samples get analyzed.
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