--- a
+++ b/softwares_config/macs2_2.2.8.config
@@ -0,0 +1,56 @@
+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.
+
+options:
+  -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