Lisa K. Johnson johnsolk

## masurca_installation_msu.sh
# 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

## contig_sigs.py
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)

## denovo_Trinity_make_gene_transcript_tables.ipynb

      
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                johnsolk
                / denovo_Trinity_make_gene_transcript_tables.ipynb
            
            
              Last active Mar 9, 2018
            
              
                Transcriptome annotation is a mess.
              
          
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## bash_tricks.sh
# 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

## agalma_tutorial_March2018.ipynb

      
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                johnsolk
                / agalma_tutorial_March2018.ipynb
            
            
              Last active Mar 6, 2018
            
          
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## agalma_test_Jetstream
(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

## recursive_wget.sh
# 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,

## outfmt6_m8_NCBI_Blastheader.txt
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

## sourmash_msu_hpcc.sh
# 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

## msu_modules_dammit.sh
# 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/
	# 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
	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)
	# 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
	(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
	# 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,
	# 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
	# 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/