remove -B flag for preseq and add instructions for preseq 3.2.0

docs/detailed-install.md

@@ -68,13 +68,44 @@ you may need to install `libgsl-dev` using: `apt install libgsl-dev` and either:
 More info can be found here:
 https://www.gnu.org/software/gsl/doc/html/usage.html#shared-libraries
 
+
+Instructions for installing preseq can be found here: https://github.com/smithlabcode/preseq
+
+```console
+wget https://github.com/smithlabcode/preseq/releases/download/v3.2.0/preseq-3.2.0.tar.gz
+tar -zxvf preseq-x.tar.gz
+```
+
+Move into the preseq directory and create a build directory:
+``` console
+cd preseq-x
+mkdir build && cd build
+```
+Run the configuration script:
+
+```console
+$ ../configure
+```
+
+You will need to enable hts support:
+
+```console
+../configure --enable-hts
+```
+If you need to install htslib, you can follow the guide here: https://github.com/samtools/htslib
+
+Compile and install the tools:
+
 ```console
-wget http://smithlabresearch.org/downloads/preseq_linux_v2.0.tar.bz2
-tar xvfj preseq_linux_v2.0.tar.bz2
+make
+make install
 ```
+
+
 Add to `PATH`!
+
 ```console
-export PATH="$PATH:/path/to/pepatac_tutorial/tools/preseq_v2.0/"
+export PATH="$PATH:/path/to/pepatac_tutorial/tools/preseq-3.2.0/build/"
 ```
 
 #### samblaster

pipelines/pepatac.py

@@ -1459,11 +1459,11 @@ def post_dup_aligned_reads(dedup_log):
         pm.timestamp("### Calculate library complexity")
 
         cmd1 = (tools.preseq + " c_curve -v -o " + preseq_output +
-                " -B " + mapping_genome_bam)
+                " " + mapping_genome_bam)
         pm.run(cmd1, preseq_output)
 
         cmd2 = (tools.preseq + " lc_extrap -v -o " + preseq_yield +
-                " -B " + mapping_genome_bam)
+                " " + mapping_genome_bam)
         pm.run(cmd2, preseq_yield, nofail=True)
 
         if os.path.exists(preseq_yield):