SQuIRE Steps:
{Build,Fetch,Clean,Map,Count,Call,Draw,Seek}
Build Installs required software
Fetch Downloads input files from UCSC
Clean Filters Repeatmasker file for Repeats of interest,
collapses overlapping repeats, and returns as BED
file.
Map Aligns RNAseq reads to STAR index allowing for
multiple alignments
Count Quantifies RNAseq reads aligning to TEs and genes
Call Performs differential expression analysis on TEs and
genes
Draw Makes bedgraphs and bedwigs from RNAseq data
Seek Retrieves sequences from chromosome fasta files
designated by BED file coordinates
optional arguments:
-h, --help show this help message and exit
--version print SQuIRE version number
however as a standard user, it does not:
[mweiner@cc-dclrilog62 ~]$ module load SQuIRE/0.9.9.9
(squire) [mweiner@cc-dclrilog62 ~]$ squire -h
Traceback (most recent call last):
File "/cm/shared/apps/SQuIRE/0.9.9.9/envs/squire/bin/squire", line 6, in
from pkg_resources import load_entry_point
File "/cm/shared/apps/SQuIRE/0.9.9.9/envs/squire/lib/python2.7/site-packages/pkg_resources/init.py", line 3251, in
@_call_aside
File "/cm/shared/apps/SQuIRE/0.9.9.9/envs/squire/lib/python2.7/site-packages/pkg_resources/init.py", line 3235, in _call_aside
f(*args, **kwargs)
File "/cm/shared/apps/SQuIRE/0.9.9.9/envs/squire/lib/python2.7/site-packages/pkg_resources/init.py", line 3264, in _initialize_master_working_set
working_set = WorkingSet._build_master()
File "/cm/shared/apps/SQuIRE/0.9.9.9/envs/squire/lib/python2.7/site-packages/pkg_resources/init.py", line 583, in _build_master
ws.require(requires)
File "/cm/shared/apps/SQuIRE/0.9.9.9/envs/squire/lib/python2.7/site-packages/pkg_resources/init.py", line 900, in require
needed = self.resolve(parse_requirements(requirements))
File "/cm/shared/apps/SQuIRE/0.9.9.9/envs/squire/lib/python2.7/site-packages/pkg_resources/init.py", line 786, in resolve
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'SQuIRE' distribution was not found and is required by the application
(squire) [mweiner@cc-dclrilog62 ~]$ which squire
/cm/shared/apps/SQuIRE/0.9.9.9/envs/squire/bin/squire
(squire) [mweiner@cc-dclrilog62 ~]$ which python
/cm/shared/apps/SQuIRE/0.9.9.9/envs/squire/bin/python
Trying to install this as an environment module for our HPC users. As root, it works:
(squire) [root@cc-dclrilog61 ~]# module load SQuIRE/0.9.9.9 (squire) [root@cc-dclrilog61 ~]# squire -h usage: squire [-h] [--version] {Build,Fetch,Clean,Map,Count,Call,Draw,Seek} ...
SQuIRE Steps: {Build,Fetch,Clean,Map,Count,Call,Draw,Seek} Build Installs required software Fetch Downloads input files from UCSC Clean Filters Repeatmasker file for Repeats of interest, collapses overlapping repeats, and returns as BED file. Map Aligns RNAseq reads to STAR index allowing for multiple alignments Count Quantifies RNAseq reads aligning to TEs and genes Call Performs differential expression analysis on TEs and genes Draw Makes bedgraphs and bedwigs from RNAseq data Seek Retrieves sequences from chromosome fasta files designated by BED file coordinates
optional arguments: -h, --help show this help message and exit --version print SQuIRE version number
however as a standard user, it does not: [mweiner@cc-dclrilog62 ~]$ module load SQuIRE/0.9.9.9 (squire) [mweiner@cc-dclrilog62 ~]$ squire -h Traceback (most recent call last): File "/cm/shared/apps/SQuIRE/0.9.9.9/envs/squire/bin/squire", line 6, in
from pkg_resources import load_entry_point
File "/cm/shared/apps/SQuIRE/0.9.9.9/envs/squire/lib/python2.7/site-packages/pkg_resources/init.py", line 3251, in
@_call_aside
File "/cm/shared/apps/SQuIRE/0.9.9.9/envs/squire/lib/python2.7/site-packages/pkg_resources/init.py", line 3235, in _call_aside
f(*args, **kwargs)
File "/cm/shared/apps/SQuIRE/0.9.9.9/envs/squire/lib/python2.7/site-packages/pkg_resources/init.py", line 3264, in _initialize_master_working_set
working_set = WorkingSet._build_master()
File "/cm/shared/apps/SQuIRE/0.9.9.9/envs/squire/lib/python2.7/site-packages/pkg_resources/init.py", line 583, in _build_master
ws.require(requires)
File "/cm/shared/apps/SQuIRE/0.9.9.9/envs/squire/lib/python2.7/site-packages/pkg_resources/init.py", line 900, in require
needed = self.resolve(parse_requirements(requirements))
File "/cm/shared/apps/SQuIRE/0.9.9.9/envs/squire/lib/python2.7/site-packages/pkg_resources/init.py", line 786, in resolve
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'SQuIRE' distribution was not found and is required by the application
(squire) [mweiner@cc-dclrilog62 ~]$ which squire
/cm/shared/apps/SQuIRE/0.9.9.9/envs/squire/bin/squire
(squire) [mweiner@cc-dclrilog62 ~]$ which python
/cm/shared/apps/SQuIRE/0.9.9.9/envs/squire/bin/python
Any thoughts?