Open abalter opened 8 years ago
taoliu
commented
7 years ago Hi @abalter, could you find out where the 'conda' installed MACS2? Especially, where is the 'egg' for MACS2? According to my knowledge of 'easyinstall', it will package actual python scripts (macs2) and the library files (such as .pyc or .o files) in 'egg' then put it somewhere (such as
taoliu
commented
7 years ago @abalter Disclaimer: I have never used miniconda so the actual .pth filename might be different. But the mechanism of this setuptools should be the same...
brianpenghe
commented
5 years ago I didn't use conda but still got the same error.
brianpenghe
commented
5 years ago This is what I got:
Traceback (most recent call last): File "/usr/local/bin/macs2", line 4, in <module> __import__('pkg_resources').run_script('MACS2==2.1.2', 'macs2') File "/usr/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 658, in run_script self.require(requires)[0].run_script(script_name, ns) File "/usr/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 1429, in run_script .format(**locals()), pkg_resources.ResolutionError: Script 'scripts/macs2' not found in metadata at '/home/ubuntu/tools/MACS2-2.1.2/MACS2-2.1.2.egg-info'
abalter
commented
5 years ago I would recommend installing with conda. Seems to work perfectly now.
(base) balter@spectre3:~/deseq-learn/taxa_filtered_data$ conda create -n macs macs2
(base) balter@spectre3:~/deseq-learn/taxa_filtered_data$ conda activate macs
(macs) balter@spectre3:~/deseq-learn/taxa_filtered_data$ which macs2
/home/balter/conda/envs/macs/bin/macs2
(macs) balter@spectre3:~/deseq-learn/taxa_filtered_data$ macs2 -h
usage: macs2 [-h] [--version]
{callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak}
...
macs2 -- Model-based Analysis for ChIP-Sequencing
positional arguments:
{callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak}
callpeak Main MACS2 Function: Call peaks from alignment
results.
bdgpeakcall Call peaks from bedGraph output. Note: All regions on
the same chromosome in the bedGraph file should be
continuous so only bedGraph files from MACS2 are
accpetable.
bdgbroadcall Call broad peaks from bedGraph output. Note: All
regions on the same chromosome in the bedGraph file
should be continuous so only bedGraph files from MACS2
are accpetable.
bdgcmp Deduct noise by comparing two signal tracks in
bedGraph. Note: All regions on the same chromosome in
the bedGraph file should be continuous so only
bedGraph files from MACS2 are accpetable.
bdgopt Operations on score column of bedGraph file. Note: All
regions on the same chromosome in the bedGraph file
should be continuous so only bedGraph files from MACS2
are accpetable.
cmbreps Combine BEDGraphs of scores from replicates. Note: All
regions on the same chromosome in the bedGraph file
should be continuous so only bedGraph files from MACS2
are accpetable.
bdgdiff Differential peak detection based on paired four
bedgraph files. Note: All regions on the same
chromosome in the bedGraph file should be continuous
so only bedGraph files from MACS2 are accpetable.
filterdup Remove duplicate reads at the same position, then save
the rest alignments to BED or BEDPE file. If you use
'--keep-dup all option', this script can be utilized
to convert any acceptable format into BED or BEDPE
format.
predictd Predict d or fragment size from alignment results.
*Will NOT filter duplicates*
pileup Pileup aligned reads with a given extension size
(fragment size or d in MACS language). Note there will
be no step for duplicate reads filtering or sequencing
depth scaling, so you may need to do certain pre/post-
processing.
randsample Randomly sample number/percentage of total reads.
refinepeak (Experimental) Take raw reads alignment, refine peak
summits and give scores measuring balance of
waston/crick tags. Inspired by SPP.
optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit
For command line options of each command, type: macs2 COMMAND -h
I install
macs2usingcondaandwhichcan find it, but MACS2 throws errors when I try to run it about not being able to find files.I'm wondering if it has something to do with my python path settings. Here they are:
Cross-posted here: https://www.biostars.org/p/216312/ and here: http://stackoverflow.com/questions/40008344/macs2-python-files-not-found-after-clean-install-with-conda