dakl
/ tensorboard_logging.py
Created
December 20, 2017 14:16
— forked from gyglim/tensorboard_logging.py
Logging to tensorboard with manually generated summaries (not relying on summary ops)
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| """Simple example on how to log scalars and images to tensorboard without tensor ops. | |
| License: Copyleft | |
| """ | |
| __author__ = "Michael Gygli" | |
| import tensorflow as tf | |
| from StringIO import StringIO | |
| import matplotlib.pyplot as plt | |
| import numpy as np |
dakl
/ provision-instance.sh
Created
July 24, 2017 19:06
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| #/usr/bin/env bash | |
| sudo apt install -y bzip2 git htop | |
| ###################################################### | |
| # FISH SHELL | |
| sudo su - | |
| echo 'deb http://download.opensuse.org/repositories/shells:/fish:/release:/2/Debian_9.0/ /' > /etc/apt/sources.list.d/fish.list | |
| apt-get update -y |
dakl
/ samtools.flagstat.log
Created
May 4, 2016 06:34
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| 11540659 + 0 in total (QC-passed reads + QC-failed reads) | |
| 6365 + 0 secondary | |
| 0 + 0 supplementary | |
| 0 + 0 duplicates | |
| 11540643 + 0 mapped (100.00%:-nan%) | |
| 11534294 + 0 paired in sequencing | |
| 5767147 + 0 read1 | |
| 5767147 + 0 read2 | |
| 11518384 + 0 properly paired (99.86%:-nan%) | |
| 11534266 + 0 with itself and mate mapped |
dakl
/ gist:40ac776ac3b7d7928dd360ad2997f27f
Created
April 22, 2016 07:52
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| Sample HS_LIBRARY_SIZE HS_PENALTY_50X PCT_TARGET_BASES_10X OFF_BAIT_BASES ON_BAIT_BASES PCT_OFF_BAIT ON_BAIT_VS_SELECTED HS_PENALTY_30X PCT_TARGET_BASES_30X READ_GROUP | |
| HS_PENALTY_40X TOTAL_READS ON_TARGET_BASES MEAN_TARGET_COVERAGE ZERO_CVG_TARGETS_PCT PCT_PF_UQ_READS BAIT_TERRITORY PCT_USABLE_BASES_ON_TARGET PCT_PF_READS LIBRARY PF_READS PCT_TARGET_BASES_2X GC_DROPOUT AT_DROPOUT PCT_TARGET_BASES_50X GENOME_SIZE PCT_PF_UQ_READS_ALIGNED FOLD_80_BASE_PENALTY HS_PENALTY_10X PCT_USABLE_BASES_ON_BAIT HS_PENALTY_20X PF_UNIQUE_READS PCT_TARGET_BASES_20X SAMPLE NEAR_BAIT_BASES TARGET_TERRITORY FOLD_ENRICHMENT PCT_TARGET_BASES_40X PCT_TARGET_BASES_100X BAIT_DESIGN_EFFICIENCY BAIT_SET HS_PENALTY_100X PCT_SELECTED_BASES MEAN_BAIT_COVERAGE PF_UQ_BASES_ALIGNED PF_UQ_READS_ALIGNED | |
| P-00017852-N-03021179-TD2-CB1 0.0 0.0 899777371.0 524812.0 0.997626 0.245107 0.0 0.0 | |
| 0.0 9609180.0 524812.0 0.899072 0.836774 1.0 1689097.0 0.000543 1.0 9609180.0 0.045124 2.779323 2.431879 0.0 3137454505.0 0.938492 ? 0.0 0.000543 0.0 960918 |
dakl
/ skewer.log
Created
February 16, 2016 14:40
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| COMMAND LINE: skewer -z -t 2 --quiet -o trimmed test_1.fastq.gz test_2.fastq.gz | |
| Input file: test_1.fastq.gz | |
| Paired file: test_2.fastq.gz | |
| trimmed: trimmed-pair1.fastq.gz, trimmed-pair2.fastq.gz | |
| Parameters used: | |
| -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC | |
| -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA | |
| -- maximum error ratio allowed (-r): 0.100 | |
| -- maximum indel error ratio allowed (-d): 0.030 |
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| ## htsjdk.samtools.metrics.StringHeader | |
| # picard.analysis.CollectOxoGMetrics INPUT=virtual-tumor.bam OUTPUT=oxog.txt REFERENCE_SEQUENCE=/proj/b2010040/private/nobackup/autoseqer-genome/genome/human_g1k_v37_decoy.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 MINIMUM_INSERT_SIZE=60 MAXIMUM_INSERT_SIZE=600 USE_OQ=true CONTEXT_SIZE=1 STOP_AFTER=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false | |
| ## htsjdk.samtools.metrics.StringHeader | |
| # Started on: Wed Feb 10 11:23:36 UTC 2016 | |
| ## METRICS CLASS picard.analysis.CollectOxoGMetrics$CpcgMetrics | |
| SAMPLE_ALIAS LIBRARY CONTEXT TOTAL_SITES TOTAL_BASES REF_NONOXO_BASES REF_OXO_BASES REF_TOTAL_BASES ALT_NONOXO_BASES ALT_OXO_BASES OXIDATION_ERROR_RATE OXIDATION_Q C_REF_REF_BASES G_REF_REF_BASES C_REF_ALT_BASES G_REF_ALT_BASES C_REF_OXO_ERROR_RATE C_REF_OXO_Q G_REF_OXO_ERROR_RATE G_REF_OXO_Q | |
| virtual-tumor virtual-tumor ACT 27 388 238 150 388 0 0 0.002577 25.888 |
dakl
/ arteria-launch.log
Created
October 21, 2015 06:16
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| $ vagrant up | |
| Bringing machine 'stackstorm-master' up with 'virtualbox' provider... | |
| Bringing machine 'testarteria1' up with 'virtualbox' provider... | |
| Bringing machine 'testuppmax' up with 'virtualbox' provider... | |
| ==> stackstorm-master: Importing base box 'ubuntu/trusty64'... | |
| ==> stackstorm-master: Matching MAC address for NAT networking... | |
| ==> stackstorm-master: Checking if box 'ubuntu/trusty64' is up to date... | |
| ==> stackstorm-master: Setting the name of the VM: arteria-provisioning_stackstorm-master_1445365324370_61846 | |
| ==> stackstorm-master: Clearing any previously set forwarded ports... | |
| ==> stackstorm-master: Fixed port collision for 22 => 2222. Now on port 2201. |
dakl
/ reportcreatormahcine.Vagrantfile
Last active
October 6, 2015 11:12
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| #Define the list of machines | |
| machines = { | |
| :reportcreatormahcine => { | |
| :hostname => "reportcreatormahcine", | |
| :ipaddress => "10.10.10.99" #gretzky | |
| }, | |
| } | |
| #-------------------------------------- | |
| # General provisioning inline script |
dakl
/ tcga-vcfs-to-pancan19.sh
Last active
November 23, 2015 14:30
Merge VCFs from 19 TCGA projects to a pancan19 VCF
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| #!/bin/bash | |
| REF=/proj/b2010040/private/nobackup/autoseqer-genome/genome/human_g1k_v37_decoy.fasta | |
| DICT=/proj/b2010040/private/nobackup/autoseqer-genome/genome/human_g1k_v37_decoy.dict | |
| GATKJAR=/home/daniel.klevebring/projects/tcga-maf-to-vcf/GenomeAnalysisTK.jar | |
| WORKDIR=$HOME/Crisp/dakl/tcga-maf-to-vcf | |
| mkdir -p $WORKDIR | |
| cd $WORKDIR | |
dakl
/ tcga-maf-to-vcf.sh
Last active
February 12, 2021 14:06
Convert TCGA MAFs to VCFs to use to annotate other VCF files with variant frequency in the various TCGA projects (including pancan12).
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| REF=/proj/b2010040/private/nobackup/autoseqer-genome/genome/human_g1k_v37_decoy.fasta | |
| DICT=/proj/b2010040/private/nobackup/autoseqer-genome/genome/human_g1k_v37_decoy.dict | |
| GATKJAR=/home/daniel.klevebring/projects/tcga-maf-to-vcf/GenomeAnalysisTK.jar | |
| WORKDIR=$HOME/Crisp/dakl/tcga-maf-to-vcf | |
| mkdir -p $WORKDIR | |
| cd $WORKDIR | |
| #unpack maf to workdir | |
| tar xvfz ~/projects/tcga-maf-to-vcf/pancan_cleaned_mafs.tar.gz |
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