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[ucsd-train25@tscc-login1 ~]$ conda env list | |
# conda environments: | |
# | |
base * /home/ucsd-train25/anaconda2 | |
deseq2-test /home/ucsd-train25/anaconda2/envs/deseq2-test | |
dropseqtools /home/ucsd-train25/anaconda2/envs/dropseqtools | |
py2_env /home/ucsd-train25/anaconda2/envs/py2_env | |
py3_cshl /home/ucsd-train25/anaconda2/envs/py3_cshl | |
seurat /home/ucsd-train25/anaconda2/envs/seurat | |
seurat-test /home/ucsd-train25/anaconda2/envs/seurat-test |
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SafetyError: The package for r-base located at /home/ucsd-train25/anaconda2/pkgs/r-base-3.4.1-1 | |
appears to be corrupted. The path 'lib/R/doc/html/packages.html' | |
has a sha256 mismatch. | |
reported sha256: 7d66db1bf6965741f31d52ee0085f61fac29983b5ba6d5372785531af39c0299 | |
actual sha256: 627828310cd1356817837e6c3197b8bd6d854ee437587c85247bac62c51a6a65 | |
done | |
Executing transaction: / dbus post-link :: /etc/machine-id not found .. | |
dbus post-link :: .. using /proc/sys/kernel/random/boot_id |
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(dropseqtools) [ucsd-train25@tscc-login1 software]$ conda develop Drop-seq_tools-1.13 | |
Traceback (most recent call last): | |
File "/home/ucsd-train25/anaconda2/bin/conda-develop", line 11, in <module> | |
sys.exit(main()) | |
File "/home/ucsd-train25/anaconda2/lib/python2.7/site-packages/conda_build/cli/main_develop.py", line 72, in main | |
return execute(sys.argv[1:]) | |
File "/home/ucsd-train25/anaconda2/lib/python2.7/site-packages/conda_build/cli/main_develop.py", line 68, in execute | |
build_ext=args.build_ext, clean=args.clean, uninstall=args.uninstall) | |
File "/home/ucsd-train25/anaconda2/lib/python2.7/site-packages/conda_build/api.py", line 292, in develop | |
return execute(recipe_dir, prefix, no_pth_file, build_ext, clean, uninstall) |
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SafetyError: The package for r-base located at /home/ucsd-train25/anaconda2/pkgs/r-base-3.4.1-1 | |
appears to be corrupted. The path 'lib/R/doc/html/packages.html' | |
has a sha256 mismatch. | |
reported sha256: 7d66db1bf6965741f31d52ee0085f61fac29983b5ba6d5372785531af39c0299 | |
actual sha256: 627828310cd1356817837e6c3197b8bd6d854ee437587c85247bac62c51a6a65 | |
ClobberError: The package 'defaults::libgcc-7.2.0-h69d50b8_2' cannot be installed due to a | |
path collision for 'lib/libgfortran.so.3'. | |
This path already exists in the target prefix, and it won't be removed by | |
an uninstall action in this transaction. The path appears to be coming from |
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import cv2 | |
import numpy as np | |
import math | |
from matplotlib import pyplot as plt | |
%matplotlib inline | |
filename = "IsoRaft_4DIV_Post_picking.png" | |
img = cv2.imread(filename) | |
plt.imshow(img, cmap='gray') |
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demux_paired_end.py --fastq_1 EW52_S45_L004_R1_001.fastq.gz \ | |
--fastq_2 EW52_S45_L004_R2_001.fastq.gz \ | |
--length 10 \ | |
-m EW52_S45.txt |
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**Array Jobs on TSCC** | |
We can specify in the submission parameters that we want to submit an array job. Here is an example. Notice the -t flag, that tells TSCC to use an array job to process this. Since we have 4 commands here, we will use -t 1-4. | |
#!/bin/bash | |
#PBS -N run_homer | |
#PBS -o run_homer.sh.out | |
#PBS -e run_homer.sh.err | |
#PBS -l walltime=5:00:00 | |
#PBS -l nodes=1:ppn=1 |
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outrigger index --sj-out-tab ../ep-cj-n2-ndiff-hs_S1_R1_001.polyATrim.adapterTrim.rmRep.bamSJ.out.tab --gtf /projeyeolab/genomes/hg19/gencode_v19/gencode.v19.annotation.gtf | |
2017-04-13 16:51:57 Creating folder ./outrigger_output ... | |
2017-04-13 16:51:57 Done. | |
2017-04-13 16:51:57 Creating folder ./outrigger_output/index ... | |
2017-04-13 16:51:57 Done. | |
2017-04-13 16:51:57 Creating folder ./outrigger_output/index/gtf ... | |
2017-04-13 16:51:57 Done. | |
2017-04-13 16:51:57 Creating folder ./outrigger_output/junctions ... | |
2017-04-13 16:51:57 Done. | |
2017-04-13 16:51:57 Found compiled junction reads file in ./outrigger_output/junctions/reads.csv and reading it in ... |
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#!/bin/env python | |
import pybedtools | |
import subprocess | |
from argparse import ArgumentParser | |
import os | |
#Todo: Need to add a check to see if the shuffled bed file already exists | |
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