| # 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 |
| # 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 |
| >DNA_CS | |
| GCCATCAGATTGTGTTTGTTAGTCGCTTTTTTTTTTTGGAATTTTTTTTTTGGAATTTTTTTTTTGCGCTAACAACCTCCTGCCGTTTTGCCCGTGCATATCGGTCACGAACAAATCTGATTACTAAACACAGTAGCCTGGATTTGTTCTATCAGTAATCGACCTTATTCCTAATTAAATAGAGCAAATCCCCTTATTGGGGGTAAGACATGAAGATGCCAGAAAAACATGACCTGTTGGCCGCCATTCTCGCGGCAAAGGAACAAGGCATCGGGGCAATCCTTGCGTTTGCAATGGCGTACCTTCGCGGCAGATATAATGGCGGTGCGTTTACAAAAACAGTAATCGACGCAACGATGTGCGCCATTATCGCCTAGTTCATTCGTGACCTTCTCGACTTCGCCGGACTAAGTAGCAATCTCGCTTATATAACGAGCGTGTTTATCGGCTACATCGGTACTGACTCGATTGGTTCGCTTATCAAACGCTTCGCTGCTAAAAAAGCCGGAGTAGAAGATGGTAGAAATCAATAATCAACGTAAGGCGTTCCTCGATATGCTGGCGTGGTCGGAGGGAACTGATAACGGACGTCAGAAAACCAGAAATCATGGTTATGACGTCATTGTAGGCGGAGAGCTATTTACTGATTACTCCGATCACCCTCGCAAACTTGTCACGCTAAACCCAAAACTCAAATCAACAGGCGCCGGACGCTACCAGCTTCTTTCCCGTTGGTGGGATGCCTACCGCAAGCAGCTTGGCCTGAAAGACTTCTCTCCGAAAAGTCAGGACGCTGTGGCATTGCAGCAGATTAAGGAGCGTGGCGCTTTACCTATGATTGATCGTGGTGATATCCGTCAGGCAATCGACCGTTGCAGCAATATCTGGGCTTCACTGCCGGGCGCTGGTTATGGTCAGTTCGAGCATAAGGCTGACAGCCTGATTGCAAAATTCAAAGAAGCGGGCGGAACGGTCAGAGAGATTGATGTATGAGCAGAGTCACCGCGATTATCTCC |
| #outputs top 20 barcodes in file, if there are any | |
| zcat lane1_sample_L001_R1_001.fastq.gz | head -400000 | grep '^@HWI' | cut -d : -f 10 | sort | uniq -c | sort -nr | head -20 |
| 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) |
| ################################################################### | |
| """Function: Take in a dammit gff3, dammit fasta, dammit namemap. | |
| Output gff3 and fasta with trinity names. | |
| by Dr. Tessa Pierce | |
| """ | |
| ################################################################### | |
| import sys | |
| import os | |
| import argparse |
Got this error message:
[ljcohen@dev-intel16 Porites_astreoites_larvae_salinity]$ git push origin master
error: The requested URL returned error: 403 Forbidden while accessing https://github.com/ljcohen/Porites_astreoites_larvae_salinity.git/info/refs
fatal: HTTP request failed
Googled problem and found this: