ecwheele

[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

ecwheele

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

ecwheele

(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)

ecwheele

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

ecwheele

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')

ecwheele

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

ecwheele

**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

ecwheele

ecwheele

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 ...

ecwheele

#!/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