Michael Schatz mschatz
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| gsutil -u anvil-tool-development du gs://fc-47de7dae-e8e6-429c-b760-b4ba49136eee > t2t.list.txt | |
| grep -v '/$' t2t.list.txt | awk '{split($2,a,"."); print a[length(a)], $1}' | grep -v 'gs:' | awk '{names[$1]++; sizes[$1]+=$2;} END{for (name in names) print name, names[name], sizes[name]}' | sort -nrk3 | head |
mschatz
/ pdfmerge.sh
Created
October 28, 2022 03:42
— forked from BeatHubmann/pdfmerge.sh
Batch merge PDF files Mac OS command line
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| gs -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sOutputFile=_all-merged.pdf *.pdf |
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| version 1.0 | |
| task untar { | |
| input { | |
| File archive | |
| } | |
| command <<< | |
| mkdir untar | |
| tar xf ~{archive} -C untar | |
| find untar -type f > filelist.txt |
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| #include <stdio.h> | |
| #include <string.h> | |
| int main(int argc, char ** argv) | |
| { | |
| char letters [] = "ABCDEFGHIJKLMNOPQRSTUVabcdefgtxxzz"; | |
| for (int i = 0; i < strlen(letters); i++) | |
| { | |
| char bp = letters[i]; |
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| ##fileformat=VCFv4.2 | |
| ##FILTER=<ID=PASS,Description="All filters passed"> | |
| ##ALT=<ID=NON_REF,Description="Represents any possible alternative allele not already represented at this location by REF and ALT"> | |
| ##FILTER=<ID=LowQual,Description="Low quality"> | |
| ##FILTER=<ID=VQSRTrancheINDEL95.00to100.00+,Description="Truth sensitivity tranche level for INDEL model at VQS Lod < -7145.7725"> | |
| ##FILTER=<ID=VQSRTrancheINDEL95.00to100.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -7145.7725 <= x < -0.0761"> | |
| ##FILTER=<ID=VQSRTrancheSNP99.80to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -66643.7516"> | |
| ##FILTER=<ID=VQSRTrancheSNP99.80to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -66643.7516 <= x < -116.7261"> | |
| ##GATKCommandLine=<ID=ApplyVQSR,CommandLine="ApplyVQSR --recal-file /cromwell_root/1kgp.chrY.recalibrate_indel.recal --tranches-file /cromwell_root/fc-51aefb1c-4e8e-4dcb-a59c-62e318ea351a/221c5800-22d5-4843-945c-1e5d4a5da0b6/ |
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| while true; do date; sleep 3; done | tee true.log |
mschatz
/ globus-cli.sh
Last active
May 11, 2021 05:02
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| $ wget https://downloads.globus.org/globus-connect-personal/linux/stable/globusconnectpersonal-latest.tgz | |
| $ tar xzvf globusconnectpersonal-latest.tgz | |
| export PYTHONHOME=~/miniconda3 | |
| ## setup and name your endpoint | |
| $ globusconnectpersonal-3.1.1/globusconnectpersonal -setup | |
| $ globusconnectpersonal-3.1.1/globusconnectpersonal -start & | |
| $ pip install globus-cli | |
| $ globus login |
mschatz
/ close_terra_billing_project.R
Created
April 27, 2021 01:48
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| library(AnVIL) | |
| terra = Terra() | |
| response = terra$listBillingProjectMembers("deeppilots-bioconductor") | |
| emails = response |> flatten() |> filter(role == "User") |> pull(email) | |
| for (email in emails) terra$removeUserFromBillingProject("deeppilots-bioconductor", "User", email) |
mschatz
/ gcloud_local_setup.sh
Last active
April 15, 2021 03:17
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| ### local install of gcloud/gsutils | |
| cd ~/build | |
| curl -O https://dl.google.com/dl/cloudsdk/channels/rapid/downloads/google-cloud-sdk-332.0.0-linux-x86_64.tar.gz | |
| tar xzvf google-cloud-sdk-332.0.0-linux-x86_64.tar.gz | |
| cd google-cloud-sdk | |
| ./install.sh | |
| . ~/.bashrc | |
| gcloud init --console-only | |
| gcloud auth application-default login --no-launch-browser |
mschatz
/ T2T Analysis
Last active
April 22, 2021 17:03
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| T2T Analysis Scripts | |
| bucketstats.R : Plot histogram of file sizes in a bucket by filetype (from gsutil ls) | |
| hcstatus.sh. : Look through buckets to see how many raw vcf files are available |
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