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@@ -0,0 +1,28 @@
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+#set username for zshrc
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+DEFAULT_USER="kheinicke"
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+
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+[[ ":$PATH:" != *":${HOME}/.local/bin:"* ]] && PATH="${HOME}/.local/bin:${PATH}"
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+export EDITOR=nvim
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+export KRB5CCNAME=$HOME/.krb5cc
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+
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+alias set_conda="source /usr/scripts/set_conda.sh && source ~/.set_conda_local"
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+alias rf="set_conda && conda activate root_forge"
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+alias ipy="set_conda && conda activate root_forge_36 && ipython"
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+
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+export CONDOR_LOGS=/ceph/users/kheinicke/condor_logs
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+export D=/ceph/users/kheinicke/b2oc/dsk-run2
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+
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+function batchmake () {
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+ mkdir -p $CONDOR_LOGS/{stderr,log,stdout}
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+ snakemake --cores 10000 --local-cores 64 --latency-wait 1 \
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+ --max-jobs-per-second 32 --max-status-checks-per-second 512 \
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+ --drmaa \
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+" getenv = True "$'\n'\
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+" request_cpus = {threads}"$'\n'\
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+" output = $CONDOR_LOGS/stdout/{rule}.{wildcards}.out"$'\n'\
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+" error = $CONDOR_LOGS/stderr/{rule}.{wildcards}.err"$'\n'\
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+" logs = $CONDOR_LOGS/log/{rule}.{wildcards}.log "$'\n'\
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+" request_memory = 8G "$'\n'\
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+" +MaxRunHours = ${MAXRUNHOURS:-24} " \
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+${*} | sed "s/DEBUG: Sleeping for a moment/./g"
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+}
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