olgabot’s gists

olgabot / exit139_command.run

Created April 17, 2020 00:23

This file has been truncated, but you can view the full file.

	#!/bin/bash
	# NEXTFLOW TASK: diff_hash (Monocyte)
	set -e
	set -u
	NXF_DEBUG=${NXF_DEBUG:=0}; [[ $NXF_DEBUG > 1 ]] && set -x
	NXF_ENTRY=${1:-nxf_main}

	nxf_tree() {
	local pid=$1

olgabot / comet_mngs_cherry_picking_samples_from_accession_ids.ipynb

Created March 24, 2020 13:23

Sorry, something went wrong. Reload?

Sorry, we cannot display this file.

Sorry, this file is invalid so it cannot be displayed.

olgabot / kill_aws_batch_jobs.ipynb

Last active November 5, 2019 13:00

Sorry, something went wrong. Reload?

Sorry, we cannot display this file.

Sorry, this file is invalid so it cannot be displayed.

olgabot / make_amplicon_fastas_for_laura.ipynb

Created May 31, 2019 01:49

Sorry, something went wrong. Reload?

Sorry, we cannot display this file.

Sorry, this file is invalid so it cannot be displayed.

olgabot / downloading_ftp_files.txt

Created February 22, 2019 21:41

pac bio nonsense






	[508/508]ubuntu@ip-172-31-15-182:~$
	ubuntu@ip-172-31-15-182:~$
	ubuntu@ip-172-31-15-182:~$ ls
	anaconda crispr_primer.py example_output.csv example_output.csv.dropout isPcr primer3_settings.cnf volume
	blat example_input.bed.csv example_output.csv.bed genome plate8primers.csv primer3_settings_dir

olgabot / reflow run error output

Created October 23, 2018 22:01

how to use trace and len of file to dynamically allocate memory

	Tue 23 Oct - 14:57  ~/code/kmer-hashing/sourmash/maca/10x_spleen_kidney   origin ☊ olgabot/search-compare-ignore-abundance ✔ 5☀ 
	 reflow run ../../../reflow/sourmash_compute_10x.rf -ksizes "21,27,33,51" -num_hashes 5000 -tenx s3://czbiohub-maca/10x_data/10X_P4_7 -output s3://olgabot-maca/10x/sourmash_compute/ksizes=21,27,33,51_num_hashes=1000/Spleen_10X_P4_7.csv
	2018/10/23 14:57:48 panic while evaluating <(signature file)>exec(decls(<string>assign(image, <string>ident("kmer_hashing")), <int>assign(mem, <int>ident("memory"))), (signature file), "\n\t\t/opt/conda/bin/sourmash compute \\\n {{protein_flag}} \\\n {{dna_flag}} \\\n --input-is-10x \\\n --processes {{processes}} \\\n --num-hashes {{num_hashes}} \\\n --ksizes {{ksizes}} \\\n --output {{signature}} \\\n {{tenx}}\n "): invalid type
	goroutine 1 [running]:
	runtime/debug.Stack(0xc4206aad50, 0xd7a240, 0x10a1670)
	/Users/marius/.gimme/versions/go1.10.darw

olgabot / 010_cosine_elbow_method.ipynb

Created September 19, 2018 19:56

Sorry, something went wrong. Reload?

Sorry, we cannot display this file.

Sorry, this file is invalid so it cannot be displayed.

olgabot / 4b1a6ae762ae00850276fee96e22333872458e2d80d0f9ea45c0acf65f77be58.bak

Last active August 9, 2018 23:07

{"ID":"sha256:4b1a6ae762ae00850276fee96e22333872458e2d80d0f9ea45c0acf65f77be58","Program":"../../reflow/sourmash_compare.rf","Params":{"ksize":"12","output":"s3://olgabot-maca/facs/sourmash_compare/trim=false_scaled=1000_dna_ksize=12.npy","sequence_to_compare":"dna","signatures":"s3://olgabot-maca/facs/sourmash_dna-only_trim=false_scaled=1000"},"Args":[],"Phase":1,"AllocID":"ec2-18-237-50-165.us-west-2.compute.amazonaws.com:9000/c7d410ce2e83574a","AllocInspect":{"ID":"c7d410ce2e83574a","Resources":{"cpu":4,"disk":1073741824,"mem":34359738368},"Meta":{"Want":{"cpu":4,"disk":1073741824,"mem":34359738368},"Owner":" \u003colga\u003e","Labels":{"ID":"4b1a6ae762ae00850276fee96e22333872458e2d80d0f9ea45c0acf65f77be58","param[ksize]":"12","param[output]":"s3://olgabot-maca/facs/sourmash_compare/trim=false_scaled=1000_dna_ksize=12.npy","param[sequence_to_compare]":"dna","param[signatures]":"s3://olgabot-maca/facs/sourmash_dna-only_trim=false_scaled=1000","program":"../../reflow/sourmash_compare.rf"}},"Created":"2018-08

olgabot / 6506e7ca189c3c141ed6302775a213910a7794f7a4f54eed3bc7172a47f87a6f.bak

Created July 25, 2018 23:06

{"ID":"sha256:6506e7ca189c3c141ed6302775a213910a7794f7a4f54eed3bc7172a47f87a6f","Program":"/Users/olgabot/code/kmer-hashing/reflow/sourmash_compare.rf","Params":{"ksize":"3","output":"s3://olgabot-maca/facs/sourmash_compare/dna-only_trim=true_scaled=100_ksize=3","sequence_to_compare":"dna","signatures":"s3://olgabot-maca/facs/sourmash_dna-only_trim=true_scaled=100"},"Args":null,"Phase":2,"AllocID":"ec2-54-148-223-208.us-west-2.compute.amazonaws.com:9000/02b31f63de8de39e","AllocInspect":{"ID":"02b31f63de8de39e","Resources":{"cpu":1,"disk":2641145643008,"intel_avx":1,"mem":3751867801},"Meta":{"Want":{"cpu":1,"disk":2641145643008,"intel_avx":1,"mem":3751867801},"Owner":"Olga Botvinnik \u003colgabot\u003e","Labels":{"ID":"6506e7ca189c3c141ed6302775a213910a7794f7a4f54eed3bc7172a47f87a6f","param[ksize]":"3","param[output]":"s3://olgabot-maca/facs/sourmash_compare/dna-only_trim=true_scaled=100_ksize=3","param[sequence_to_compare]":"dna","param[signatures]":"s3://olgabot-maca/facs/sourmash_dna-only_trim=true_scaled=1

olgabot / 7bf6d67e11a38f11e301e3fe7f14489a11f350e6a833c54281c551f78c894fbf.bak

Created July 18, 2018 23:02

{"ID":"sha256:7bf6d67e11a38f11e301e3fe7f14489a11f350e6a833c54281c551f78c894fbf","Program":"/Users/olgabot/code/kmer-hashing/reflow/sourmash_index.rf","Params":{"ksize":"3","output":"s3://olgabot-maca/facs/sourmash_index/dna-only_trim=true_scaled=100_ksize=3","sequence_to_compare":"dna","signatures":"s3://olgabot-maca/facs/sourmash_dna-only_trim=true_scaled=100"},"Args":null,"Phase":1,"AllocID":"ec2-34-221-195-240.us-west-2.compute.amazonaws.com:9000/126a7a34276c2d1f","AllocInspect":{"ID":"126a7a34276c2d1f","Resources":{"cpu":1,"disk":1073741824,"mem":17179869184},"Meta":{"Want":{"cpu":1,"disk":1073741824,"mem":17179869184},"Owner":"Olga Botvinnik \u003colgabot\u003e","Labels":{"ID":"7bf6d67e11a38f11e301e3fe7f14489a11f350e6a833c54281c551f78c894fbf","param[ksize]":"3","param[output]":"s3://olgabot-maca/facs/sourmash_index/dna-only_trim=true_scaled=100_ksize=3","param[sequence_to_compare]":"dna","param[signatures]":"s3://olgabot-maca/facs/sourmash_dna-only_trim=true_scaled=100","program":"/Users/olgabot/code/kme

Olga Botvinnik olgabot