Update dependencies

README.md

@@ -70,8 +70,8 @@ of the pipeline. The following options are available:
 
 - `-o|--organism` (default: `human`): Organism to run ROP for.
     - Exactly one of the following: human, mouse.
-- `-s|--steps` (default: all except lowq and bacteria): Select the analysis
-  modes to use.
+- `-s|--steps` (default: all except lowq, metaphlan, bacteria): Select the
+  analysis modes to use.
     - A comma-separated list of one or more of the following: lowq, rdna,
       reference, repeats, circrna, immune, microbiome (which may be subdivided
       into bacteria, metaphlan, viral, fungi, protozoa).

environment.yml

@@ -12,10 +12,11 @@ dependencies:
     - bowtie2
     - bwa
     - fastx_toolkit
-    - intervaltree
     - jellyfish
     - pysam
     - samtools
     - tophat
     - pip:
+        - intervaltree
+        - networkx
         - tools/suffix_tree-2.1.tar.gz

rop.sh

@@ -45,8 +45,8 @@ eval set -- "$PARSED"
 
 # Set default options.
 ORGANISM='human'
-STEPS='rdna reference repeats immune metaphlan viral fungi protozoa'
-    # Non-default: lowq (too slow).
+STEPS='rdna reference repeats immune viral fungi protozoa'
+    # Non-default: metaphlan (temporarily broken), lowq (slow).
     # Disabled: circrna bacteria (databases missing).
 FASTA=false
 BAM=false

tools/install-MiniConda.sh

@@ -10,11 +10,11 @@ InstallDir="MiniConda"
 # Dependencies installed by Conda
 # Comment out the next line if no Conda dependencies
 CondaDeps="biopython numpy scipy scikit-learn pandas"
-BiocondaDeps="blast bowtie2 bwa fastx_toolkit intervaltree jellyfish pysam samtools tophat"
+BiocondaDeps="blast bowtie2 bwa fastx_toolkit jellyfish pysam samtools tophat"
 
 # Install the package from PyPi
 # Comment out next line if installing locally
-PyPiPackage="biopython networkx"
+PyPiPackage="intervaltree networkx"
 
 # Local packages to install
 # Useful if your application is not in PyPi