Skip to content

Instantly share code, notes, and snippets.

View johnsolk's full-sized avatar

Lisa K. Johnson johnsolk

85 followers · 70 following
View GitHub Profile
@johnsolk
johnsolk / jupyter_farm.sh
Last active July 24, 2018 23:50
# 10/19/2017, with help from Luiz Irber
# ssh ljcohen@farm.cse.ucdavis.edu
# start interactive job, get assigned a designated compute node
# srun -p high -t 24:00:00 --mem=20000 --pty bash
# on the farm cluster
# jupyter notebook is installed in anaconda, in home dir
# activate virtualenv
source ~/anaconda2/envs/py3.dammit/bin/activate
# change environment variable to change where tmp files are stored
export XDG_RUNTIME_DIR=/home/ljcohen/tmp
@johnsolk
johnsolk / mmetsp_loops.sh
Created October 26, 2017 00:12
for file in $(find . -name "*.fasta.dammit.gff3"); do echo $file; cut -f1 $file | uniq | wc -l; done > ~/MMETSP/assembly_evaluation_data/total_contigs
for file in $(find `pwd` -name "*.fasta.renamed.fasta.dammit.gff3");
do
base=$(basename $file .renamed.fasta.dammit.gff3)
new=$base.dammit.gff3
echo cp $file /mnt/scratch/ljcohen/mmetsp_dammit/cp/gff3/$new
done
@johnsolk
johnsolk / Notes.md
Created October 31, 2017 16:14

  • labeled text MA plot

  • Fun fact: suspended gold in the ocean, mostly from hydrothermal vents, is enough for each person on Earth to have 9 lbs. - Microbial Diversity, 2017

  • "You don't have to be great at something to do it or enjoy doing it!" You can keep doing it. - Tracy Teal

@johnsolk
johnsolk / add_path.sh
Created November 1, 2017 21:23
# add current directory to ~/.bashrc
echo export PATH=$PATH:$(pwd) >> ~/.bashrc
source ~/.bashrc
@johnsolk
johnsolk / msu_modules_dammit.sh
Created November 5, 2017 01:02
# load these modules to run dammit on MSU HPCC
source /mnt/home/ljcohen/.bashrc
module load GNU/4.8.3
module unload python
module load anaconda
module load parallel
source activate dammit
module load LAST/737
export DAMMIT_DB_DIR=/mnt/research/ged/data/dammitdb/
@johnsolk
johnsolk / sourmash_msu_hpcc.sh
Last active November 29, 2017 20:00
# load modules
module load GNU/4.8.3 anaconda parallel
module unload python
# setup conda env
conda create --name sourmash_nov2017 python=3.5
# use this to activate env:
source activate sourmash_nov2017
@johnsolk
johnsolk / outfmt6_m8_NCBI_Blastheader.txt
Created January 19, 2018 20:45 — forked from Verrus/outfmt6_m8_NCBI_Blastheader.txt
NCBI Blast output header -outfmt 6 or -m8 header in tabular form
query_id subject_id pct_identity aln_length n_of_mismatches gap_openings q_start q_end s_start s_end e_value bit_score
@johnsolk
johnsolk / recursive_wget.sh
Created February 21, 2018 19:18
# password required
wget -r -l1 --no-parent --user=user --password=password http://server.server.edu/path/to/files/
# no password required
wget -r -l1 --no-parent --no-check-certificate https://server.server.edu/path/to/files
# If ftp server, with user and password required:
wget -r --user XXX --password XXX ftp://1234.5678.10
# Login to ftp server,
@johnsolk
johnsolk / agalma_test_Jetstream
Created March 5, 2018 20:35
(agalma) ljcohen@js-169-78:~/tmp$ agalma test
Created temp directory '/home/ljcohen/tmp/agalma-test-transcriptome-VE7'
biolite.config.parse_env_resources: database=/home/ljcohen/tmp/agalma-test-transcriptome-VE7/agalma.sqlite
biolite.utils.safe_mkdir: directory '/home/ljcohen/tmp/agalma-test-transcriptome-VE7' already exists
SRX288285 [2018-03-05 20:03:47]
/home/ljcohen/tmp/agalma-test-transcriptome-VE7/SRX288285_1.fq.gz (3.6 MB)
/home/ljcohen/tmp/agalma-test-transcriptome-VE7/SRX288285_2.fq.gz (3.7 MB)
species: Agalma elegans
ncbi_id: 316166
itis_id: None
@johnsolk
johnsolk / agalma_tutorial_March2018.ipynb
Last active March 6, 2018 16:46
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.