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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
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"You don't have to be great at something to do it or enjoy doing it!" You can keep doing it. - Tracy Teal
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# 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 |
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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 |
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# add current directory to ~/.bashrc | |
echo export PATH=$PATH:$(pwd) >> ~/.bashrc | |
source ~/.bashrc |
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# 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/ |
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# 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 |
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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 |
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# 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, |
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(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 |
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