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Lisa K. Johnson johnsolk

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johnsolk / masurca_installation_msu.sh
Created July 20, 2018 21:51
# MaSuRCA 3.2.6 installation on MSU hpcc
ssh dev-intel14
cd bin
wget https://github.com/alekseyzimin/masurca/releases/download/3.2.6/MaSuRCA-3.2.6.tar.gz
tar -xvzf MaSuRCA-3.2.6.tar.gz
cd MaSuRCA-3.2.6
module load GNU/4.8.3
BOOST_ROOT=install ./install.sh
@johnsolk
johnsolk / contig_sigs.py
Last active September 17, 2018 23:21
import screed
import os
from os import path
import subprocess
from subprocess import Popen, PIPE
def make_dir(dirname):
if os.path.isdir(dirname) == False:
os.mkdir(dirname)
print("Directory created:", dirname)
@johnsolk
johnsolk / denovo_Trinity_make_gene_transcript_tables.ipynb
Last active March 9, 2018 19:30
Transcriptome annotation is a mess.
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@johnsolk
johnsolk / bash_tricks.sh
Last active March 6, 2018 23:20
# makes all files read only
chmod -w *
# renames files with underscores
for i in *.fastq; do j=$(echo $i | cut -d_ -f1-3 ); k=$(echo $i | cut -d_ -f5); echo mv $i "$j-$k"; done
# adds pwd to $PATH in .bashrc
echo export PATH=$(pwd):$PATH >> ~/.bashrc
# renames files
@johnsolk
johnsolk / agalma_tutorial_March2018.ipynb
Last active March 6, 2018 16:46
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@johnsolk
johnsolk / agalma_test_Jetstream
Created March 5, 2018 20:35
(agalma) ljcohen@js-169-78:~/tmp$ 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 / 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 / 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 / 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 / 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/