| function aws_switch { | |
| last_profile=$(cat ~/.aws/.last_profile | xargs) | |
| last_profile_i=1; | |
| i=1 | |
| profiles=() | |
| for profile in $(grep "^\[.*\]$" ~/.aws/credentials | sed -e 's_^\[__' -e 's_\]$__' | sort) | |
| do | |
| echo "[$i] $profile"; | |
| profiles+=( "$profile" ); |
Snapshot repository: https://oss.sonatype.org/content/repositories/snapshots/com/fulcrumgenomics/dagr-tasks_2.12/1.1.0-2d84ae1-SNAPSHOT/
Added repositories for in my build.sc:
def repositories = super.repositories ++ Seq(
coursier.LocalRepositories.Dangerous.maven2Local,
MavenRepository("https://oss.sonatype.org/content/repositories/public"),
MavenRepository("https://oss.sonatype.org/content/repositories/snapshots"),
MavenRepository("https://jcenter.bintray.com/")
| [2019/08/20 23:31:03 | SortPrimerPairs | Info] Wrote 2,400,000,000 primer pairs. Elapsed time: 07:37:04s. Time for last 2,000,000: 14s. Last read position: chrY:13,479,780 |
| #!/bin/bash | |
| set -euo pipefail | |
| # Concatenate the FASTQs per sub-read prior to running DemuxFastqs | |
| cat SAMPLE1_S1_L001_R1_001.fastq.gz SAMPLE1_S1_L001_R1_002.fastq.gz > SAMPLE1_S1_L001_R1_COMBINED.fastq.gz; | |
| cat SAMPLE1_S1_L001_R2_001.fastq.gz SAMPLE1_S1_L001_R2_002.fastq.gz > SAMPLE1_S1_L001_R2_COMBINED.fastq.gz; | |
| # Run Demux Fastqs (try `conda install -c bioconda fgbio` to install `fgbio`). | |
| # Note: since we have two sub-reads, we must have two read structures. |
| #!/bin/bash | |
| set -euo pipefail | |
| fgbio_cmd="java -Xmx8G -jar /Users/nhomer/git/fg/fgbio/target/scala-2.12/fgbio-0.8.0.jar" | |
| function build_it () | |
| { | |
| local src_build=$1; | |
| local target_build=$2; |
| >M1 | |
| CATAAAAGAACGTAGGTCGCCCGTCCGTAACCTGTCGGATCACCGGAAAGGACCCGTAAAGTGATAATGAT | |
| ATAAAGGCAGTCGCTCTGTAAGCTGTCGATTCACCGGAAAGATGGCGTTACCACGTAAAGTGATAATGATTAT | |
| ATCAAAGAACGTGTAGCCTGTCCGTAATCTAGCGCATTTCACACGAGACCCGCGTAATGGG | |
| CGTAAATAGGTAATGATTATCATTACATATCACAACTAGGGCCGTATTAATCATGATATCATCA | |
| GTCGCTAGAGGCATCGTGAGTCGCTTCCGTACCGCAAGGATGACGAGTCACTTAAAGTGATAAT | |
| CCGTAACCTTCATCGGATCACCGGAAAGGACCCGTAAATAGACCTGATTATCATCTACAT | |
| >M2 | |
| CATAAAAGAACGTAGGTCGCCCGTCCGTAACCTGTCGGATCACCGGAAAGGACCCGTAAAGTGATAATGAT | |
| ATAAAGGCAGTCGCTCTGTAAGCTGTCGATTCACCGGAAAGATGGCGTTACCACGTAAAGTGATAATGATTAT |
| #!/bin/python | |
| import sys | |
| import argparse | |
| from pathlib import Path | |
| from collections import OrderedDict | |
| import math | |
| units_and_size = [ | |
| ('Bytes', 1), |
| /* | |
| * The MIT License | |
| * | |
| * Copyright (c) 2017 Fulcrum Genomics LLC | |
| * | |
| * Permission is hereby granted, free of charge, to any person obtaining a copy | |
| * of this software and associated documentation files (the "Software"), to deal | |
| * in the Software without restriction, including without limitation the rights | |
| * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
| * copies of the Software, and to permit persons to whom the Software is |