IMPORTANT: You may need to close and restart your shell after running 'conda init'.Ĭheck if you have a section called conda initialize in the file ~/.bashrc and remove it. See 'conda init -help' for more information and options.
More information here in the Snakemake FAQ.ĬommandNotFoundError: Your shell has not been properly configured to use 'conda activate'. This is a minimal example for a rule that launches fastqc:Įxpand("qc/fastqc/ Moreover, if you launch snakemake inside a shell script, you need add the following line at the beginning of your script: As a reminder, the list of available environments is accessible with: In your snakemake rules, you can now use the conda environments with: conda activate my_env. Shell.prefix("source /usr/local/genome/Anaconda3/etc/profile.d/conda.sh ") To do this, add these lines at the beginning of your Snakefile: To use a conda environment, it is necessary to tell snakemake to load the profile.d/conda.sh. bwa.1' for the manual.Īnd to leave conda conda to use a conda environment within my snakemake workflow? Nun können Sie die Serverdaten eintragen. Wählen Sie anschließend 'Neuer Server' aus. Path has to be prefixed with 0 for user defined entries or 1 for default entries. Öffnen Sie FileZilla und klicken Sie oben links auf den 'Servermanager'. If you are not sure which to use, try `bwa mem'įirst. Any slash or backslash that is part of a segment has to be escaped with a backslash. There are three alignment algorithms in BWA: `mem', `bwasw', and Note: To use BWA, you need to first index the genome with `bwa index'. Pac2bwtgen alternative algorithm for generating BWT Pemerge merge overlapping paired ends (EXPERIMENTAL) Program: bwa (alignment via Burrows-Wheeler transformation)Ĭommand: index index sequences in the FASTA formatįastmap identify super-maximal exact matches To use bwa with conda, you need to activate the bwa conda activate bwa-0.7.17
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