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olgabot / README
Created January 27, 2015 17:40
This readme should help you get started with "pfam_scan.pl", which is for use
with the HMMER3 version of HMMER.
--------------------------------------------------------------------------------
- Setting up -------------------------------------------------------------------
--------------------------------------------------------------------------------
Unpack the script
=================
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olgabot / test_predict.py
Created June 25, 2014 20:28
How to check for raising an error within a test class using pytest?
import numpy as np
import numpy.testing as npt
import pandas as pd
import pandas.util.testing as pdt
import pytest
from sklearn.ensemble import ExtraTreesRegressor, ExtraTreesClassifier
from sklearn.preprocessing import LabelEncoder
class TestPredictorBase:
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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=$1
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olgabot / comet_mngs_cherry_picking_samples_from_accession_ids.ipynb
Created March 24, 2020 13:23
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olgabot / kill_aws_batch_jobs.ipynb
Last active November 5, 2019 13:00
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olgabot / make_amplicon_fastas_for_laura.ipynb
Created May 31, 2019 01:49
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olgabot / downloading_ftp_files.txt
Created February 22, 2019 21:41
pac bio nonsense
[508/508]ubuntu@ip-172-31-15-182:~$
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
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olgabot / Implementing design principles in matplotlib
Last active November 21, 2018 17:20
UCSD Scientific Python User Group presentation April 10th, 2013: Implementing design principles in matplotlib
This file has been truncated, but you can view the full file.
{
"metadata": {
"name": "design_with_bokeh"
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
{
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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
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olgabot / 010_cosine_elbow_method.ipynb
Created September 19, 2018 19:56
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