johnsolk

# 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

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

# 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) 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

# 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

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

# 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

# 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/