Merge pull request #1 from karolisr/main

Edits to the install script and documentation.
gladshire · Jun 23, 2024 · cc8fc9b · cc8fc9b
2 parents 475aadc + b87eff0
commit cc8fc9b
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diff --git a/.gitignore b/.gitignore
@@ -31,3 +31,4 @@ bin/*
 semblans_fa/*
 plant_cdna/*
 project/*
+*.code-workspace
diff --git a/README.md b/README.md
@@ -12,32 +12,53 @@ Through the collation of several external packages and the leveraging of C++ dat
 
 All documentation for Semblans can be found in the [wiki](https://github.com/gladshire/Semblans/wiki)
 
+# Dependencies
+
+Semblans will install most of the dependencies it requires, but make sure you have working installations of:
+- [**bowtie2**](https://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
+- [**jellyfish**](https://genome.umd.edu/jellyfish.html)
+- [**salmon**](https://salmon.readthedocs.io/en/latest/salmon.html)
+- [**samtools**](http://www.htslib.org)
+- [**numpy**](https://numpy.org)
+
+On Ubuntu this can be done by running:
+```bash
+sudo apt update
+sudo apt install bowtie2 jellyfish salmon samtools python3-numpy
+```
+
 # Installation
 
 If the user has downloaded a pre-compiled Semblans release, this step is not necessary. To install Semblans, navigate to its root directory and then call:
-```
+```bash
 ./install.sh
 ```
 Please allow several minutes for Semblans to set up the necessary packages.
 
 By default, Semblans will not retrieve the PantherDB functional protein database for sequence annotation. **If the user intends to utilize Semblans' annotation functionality, they should instead call the following installation command:
-```
+```bash
 ./install.sh --with-panther
 ```
 **Be aware that the PantherDB database is large (~17GB compressed; ~80GB uncompressed), and can take some time to download.**
 
 # Quick Start / Test data
 
 Included with Semblans is a directory called 'examples'. This directory contains a very small short read dataset ("ChloroSubSet") for testing/verifying functionality of the Semblans pipeline. To test, uncompress the data from **ChloroSubSet.tar.gz**. The user should then **ensure they have a reference proteome**, as one is necessary for several of the pipeline's postprocessing stages. Links to broad, kingdom-level reference proteomes are hosted at the bottom of this document. In this example, I use the kingdom-level plant proteome. Once prepared, the user may call:
-```
-semblans --left ChloroSubSet_1.fq --right ChloroSubSet_2.fq --prefix ChloroSubSet --ref-proteome ensembl_plant.pep.all.fa --threads 8 --ram 10
+```bash
+semblans \
+--left ChloroSubSet_1.fq \
+--right ChloroSubSet_2.fq \
+--prefix ChloroSubSet \
+--ref-proteome ensembl_plant.pep.all.fa \
+--threads 4 \
+--ram 10
 ```
 Some users may experience issues, particularly during the transcript assembly phase during Trinity. Common errors and solutions are hosted on our GitHub's [wiki page](https://github.com/gladshire/Semblans/wiki/Common-Errors-&-Solutions#issues-at-trinity-stage). As cataloguing these is an ongoing process, we urge users to post an issue on the Semblans repository page detailing their problem if it persists or is otherwise unaddressed by this page.
 
 Reference peptide sets for **postprocess**
 
-[**Ensembl animal reference**](https://uofi.app.box.com/s/0rlp6q0u5uvc161mzbdr3c0xoiti63sk)
+[**Ensembl animal reference**](https://www.dropbox.com/scl/fi/n49jm9i1yscrfrsj1dnq8/ensembl_animals.pep.all.fa.gz?rlkey=yemush6bm36wr4fu7dpe8h5e0&st=98kgb83l&dl=1)
 
-[**Ensembl plant reference**](https://uofi.app.box.com/s/lvg7x2qrxvg8hfcmue9xv4y9t1rgfb48)
+[**Ensembl plant reference**](https://www.dropbox.com/scl/fi/hbvtnd9wsiwt8k7gakcmq/ensembl_plant.pep.all.fa.gz?rlkey=8cp9sn5wrt9uu4vc2pmg8xvin&st=1gesuqq0&dl=1)
 
-[**Ensembl fungi reference**](https://uofi.box.com/s/qc4nmun4apb0pik5fqxukn4qvn3wm943)
+[**Ensembl fungi reference**](https://www.dropbox.com/scl/fi/8as6tci331utcrqrl7txz/ensembl_fungi.pep.all.fa.gz?rlkey=eyhsv35lelnao5xgd7s9dy51e&st=oc9dz9s6&dl=1)
diff --git a/install.sh b/install.sh
@@ -1,4 +1,14 @@
-#!/bin/bash
+#!/usr/bin/env bash
+####################################################
+# Suppress printing of error messages
+# exec 2>/dev/null
+# Stop on first error
+set -o errexit
+# Set trap on ERR to be inherited by shell functions
+set -o errtrace
+# Trap errors
+trap 'echo Error at line: $LINENO' ERR
+####################################################
 
 # Determine whether to install PANTHER for annotation
 install_panther=false
@@ -12,7 +22,6 @@ for flag in "$@"; do
   fi
 done
 
-
 echo "Initiating install of Semblans"
 
 if $install_panther
@@ -24,12 +33,15 @@ else
   echo "If user wishes to perform annotations, they should include the --with-panther / -p flag."
 fi
 
-# Prepare Semblans file structure
-mkdir include &>/dev/null
-mkdir lib &>/dev/null
-mkdir external &>/dev/null
+# Prepare Semblans directory structure
+rm -rf ./include ./lib ./external ./data
+
+mkdir -p ./include
+mkdir -p ./lib
+mkdir -p ./external
+
 if $install_panther; then
-	mkdir data &>/dev/null
+	mkdir -p ./data
 fi
 
 #========================================================================
@@ -39,18 +51,16 @@ fi
 echo "Now installing required libraries"
 
 # Install boost libraries
-if ( [ ! -f ./lib/libboost_filesystem.a ] ||
-     [ ! -f ./lib/libboost_regex.a ] ||
-     [ ! -f ./lib/libboost_system.a ] ||
-     [ ! -f ./lib/libboost_locale.a ] ); then
+if  [ ! -f ./lib/libboost_filesystem.a ] ||
+    [ ! -f ./lib/libboost_regex.a ] ||
+    [ ! -f ./lib/libboost_system.a ] ||
+    [ ! -f ./lib/libboost_locale.a ]; then
 	echo "  Installing Boost libraries ..."
 	wget -q https://boostorg.jfrog.io/artifactory/main/release/1.81.0/source/boost_1_81_0.tar.gz
 	tar -xf boost_1_81_0.tar.gz
-	cd boost_1_81_0
+	cd boost_1_81_0 || return 1
 	./bootstrap.sh --prefix=../
 	./b2 install cxxflags="-std=c++11" link=static
-	make
-	make install
 	mv LICENSE_1_0.txt ../include/boost/
 	cd ..
 	rm -rf boost_1_81_0*
@@ -73,13 +83,13 @@ fi
 echo "  Installing libconfini library ..."
 wget -q https://github.com/madmurphy/libconfini/releases/download/1.16.4/libconfini-1.16.4-x86_64-bin.tar.xz
 tar -xf libconfini-1.16.4-x86_64-bin.tar.xz
-mkdir ./include/libconfini
+mkdir -p ./include/libconfini
 mv ./usr/include/* ./include/libconfini/
 mv ./usr/lib/* ./lib/
 mv ./usr/share/doc/libconfini/AUTHORS ./include/libconfini/
 mv ./usr/share/doc/libconfini/COPYING ./include/libconfini/
 rm libconfini-1.16.4-x86_64-bin.tar.xz
-rm -rf ./usr/
+rm -rf ./usr
 
 # Install libcurl
 echo " Installing libcurl library ..."
@@ -102,7 +112,7 @@ if [ ! -e "./external/hmmer/bin/hmmscan" ]; then
 	wget -q http://eddylab.org/software/hmmer/hmmer.tar.gz
 	tar -xf hmmer.tar.gz -C ./external/
 	mv ./external/hmmer* ./external/hmmer
-	cd ./external/hmmer
+	cd ./external/hmmer || return 1
 	./configure --prefix "$PWD"
 	make
 	make install
@@ -132,13 +142,13 @@ fi
 
 
 # Install NCBI sra-tools
-if ( [ ! -e "./external/sratoolkit/bin/prefetch" ] &&
-     [ ! -e "./external/sratoolkit/bin/fasterq-dump" ] ); then
+if  [ ! -e "./external/sratoolkit/bin/prefetch" ] &&
+    [ ! -e "./external/sratoolkit/bin/fasterq-dump" ]; then
 	echo "Installing SRA-Tools ..."
 	wget -q --output-document sratoolkit.tar.gz https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz
 	tar -xf sratoolkit.tar.gz -C ./external/
 	mv ./external/sratoolkit* ./external/sratoolkit
-	cd ./external/sratoolkit
+	cd ./external/sratoolkit || return 1
 	wget -q https://raw.githubusercontent.com/ncbi/sra-tools/master/LICENSE
 	cd ../../
 	rm sratoolkit.tar.gz
@@ -163,9 +173,9 @@ if [ ! -e "./external/Rcorrector/rcorrector" ]; then
 	wget -q --output-document rcorrector.tar.gz https://github.com/mourisl/Rcorrector/archive/refs/tags/v1.0.7.tar.gz
 	tar -xf rcorrector.tar.gz -C ./external/
 	mv ./external/Rcorrector* ./external/Rcorrector
-	cd ./external/Rcorrector
+	cd ./external/Rcorrector || return 1
 	make
-	cd ../../
+	cd ../..
 	rm rcorrector.tar.gz
 else
 	echo "Rcorrector already installed. Skipping ..."
@@ -177,9 +187,9 @@ if [ ! -e "./external/Trimmomatic/trimmomatic-0.39.jar" ]; then
 	wget -q --output-document trimmomatic.zip http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip
 	unzip trimmomatic.zip -d ./external/
         mv ./external/Trimmomatic* ./external/Trimmomatic
-	cd ./external/Trimmomatic/adapters/
+	cd ./external/Trimmomatic/adapters || return 1
 	echo -e "$(cat NexteraPE-PE.fa)\n$(cat TruSeq2-PE.fa)\n$(cat TruSeq2-SE.fa)\n$(cat TruSeq3-PE-2.fa)\n$(cat TruSeq3-PE.fa)\n$(cat TruSeq3-SE.fa)" > TruSeq_all.fa
-	cd ../../../
+	cd ../../..
 	rm trimmomatic.zip
 else
 	echo "Trimmomatic already installed. Skipping ..."
@@ -191,9 +201,9 @@ if [ ! -e "./external/kraken2/kraken2" ]; then
 	wget -q --output-document kraken2.tar.gz https://github.com/DerrickWood/kraken2/archive/refs/tags/v2.1.2.tar.gz
 	tar -xf kraken2.tar.gz -C ./external/
 	mv ./external/kraken2-2.1.2 ./external/kraken2
-	cd ./external/kraken2
+	cd ./external/kraken2 || return 1
 	./install_kraken2.sh .
-	cd ../../
+	cd ../..
 	rm kraken2.tar.gz
 else
 	echo "Kraken2 already installed. Skipping ..."
@@ -205,19 +215,19 @@ if [ ! -e "./external/trinityrnaseq/Trinity" ]; then
 	wget -q --output-document trinity.tar.gz https://github.com/trinityrnaseq/trinityrnaseq/releases/download/Trinity-v2.15.1/trinityrnaseq-v2.15.1.FULL.tar.gz
 	tar -xf trinity.tar.gz -C ./external/
 	mv ./external/trinityrnaseq-v2.15.1 ./external/trinityrnaseq
-	cd ./external/trinityrnaseq/trinity-plugins/bamsifter
+	cd ./external/trinityrnaseq/trinity-plugins/bamsifter || return 1
 	sed -i '1s/^/#include <string> \n/' sift_bam_max_cov.cpp
-	cd ../../
+	cd ../..
 	make
-	cd ../../
+	cd ../..
 	rm trinity.tar.gz
 else
 	echo "Trinity already installed. Skipping ..."
 fi
 
 # Install NCBI BLAST
-if ( [ ! -e "./external/ncbi-blast+/bin/blastx" ] ||
-     [ ! -e "./external/ncbi-blast+/bin/blastp" ] ); then
+if [ ! -e "./external/ncbi-blast+/bin/blastx" ] ||
+   [ ! -e "./external/ncbi-blast+/bin/blastp" ]; then
 	echo "Installing NCBI-BLAST+ ..."
 	wget -q --output-document ncbi-blast.tar.gz https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.15.0/ncbi-blast-2.15.0+-x64-linux.tar.gz
 	tar -xf ncbi-blast.tar.gz -C ./external/
@@ -228,67 +238,67 @@ else
 fi
 
 # Install Diamond
-if ( [ ! -e "./external/diamond/diamond" ] ); then
+if [ ! -e "./external/diamond/diamond" ]; then
 	echo "Installing Diamond ..."
-	mkdir ./external/diamond-2.1.7
+	mkdir -p ./external/diamond-2.1.7
 	wget -q --output-document diamond.tar.gz https://github.com/bbuchfink/diamond/releases/download/v2.1.7/diamond-linux64.tar.gz
 	tar -xf diamond.tar.gz -C ./external/diamond-2.1.7/
 	mv ./external/diamond-2.1.7 ./external/diamond
-	cd ./external/diamond
+	cd ./external/diamond || return 1
 	wget -q https://raw.githubusercontent.com/bbuchfink/diamond/master/LICENSE
-	cd ../../
+	cd ../..
 	rm diamond.tar.gz
 else
 	echo "Diamond already installed. Skipping ..."
 fi
 
 
 # Install Corset
-if ( [ ! -e "./external/corset/corset" ] ); then
+if [ ! -e "./external/corset/corset" ]; then
 	echo "Installing Corset ..."
 	wget -q --output-document corset.tar.gz https://github.com/Oshlack/Corset/releases/download/version-1.09/corset-1.09-linux64.tar.gz
 	tar -xf corset.tar.gz -C ./external/
 	mv ./external/corset-1.09-linux64 ./external/corset
-	cd ./external/corset/
+	cd ./external/corset || return 1
 	chmod -x LICENSE
 	chmod -x COPYING
-	cd ../../
+	cd ../..
 	rm corset.tar.gz
 else
 	echo "Corset already installed. Skipping ..."
 fi
 
 # Install STAR
-#if ( [ ! -e "./external/STAR/bin" ] ); then
-#	echo "Installing STAR ..."
-#	wget -q --output-document star.tar.gz https://github.com/alexdobin/STAR/archive/refs/tags/2.7.11a.tar.gz
-#	tar -xf star.tar.gz -C ./external/
-#	mv ./external/STAR* ./external/STAR
-#	cd ./external/STAR/source/
-#	make STAR
-#	cd ../../../
-#	rm star.tar.gz
-#else
-#	echo "STAR alread installed. Skipping ..."
-#fi
+# if [ ! -e "./external/STAR/bin" ]; then
+# 	echo "Installing STAR ..."
+# 	wget -q --output-document star.tar.gz https://github.com/alexdobin/STAR/archive/refs/tags/2.7.11a.tar.gz
+# 	tar -xf star.tar.gz -C ./external/
+# 	mv ./external/STAR* ./external/STAR
+# 	cd ./external/STAR/source || return 1
+# 	make STAR
+# 	cd ../../..
+# 	rm star.tar.gz
+# else
+# 	echo "STAR alread installed. Skipping ..."
+# fi
 
 # Install Salmon
-if ( [ ! -e "./external/salmon/bin/salmon" ] ); then
+if [ ! -e "./external/salmon/bin/salmon" ]; then
 	echo "Installing Salmon ..."
 	wget -q --output-document salmon.tar.gz https://github.com/COMBINE-lab/salmon/releases/download/v1.10.0/salmon-1.10.0_linux_x86_64.tar.gz
 	tar -xf salmon.tar.gz -C ./external/
 	mv ./external/salmon* ./external/salmon
-	cd ./external/salmon
+	cd ./external/salmon || return 1
 	wget -q https://raw.githubusercontent.com/COMBINE-lab/salmon/master/LICENSE
-	cd ../../
+	cd ../..
 	rm salmon.tar.gz
 else
 	echo "Salmon already installed. Skipping ..."
 fi
 
 # Install TransDecoder
-if ( [ ! -e "./external/TransDecoder/TransDecoder.LongOrfs" ] ||
-     [ ! -e "./external/TransDecoder/TransDecoder.Predict" ] ); then
+if [ ! -e "./external/TransDecoder/TransDecoder.LongOrfs" ] ||
+   [ ! -e "./external/TransDecoder/TransDecoder.Predict" ]; then
 	echo "Installing TransDecoder ..."
 	wget -q --output-document transdecoder.tar.gz https://github.com/TransDecoder/TransDecoder/archive/refs/tags/TransDecoder-v5.7.0.tar.gz
 	tar -xf transdecoder.tar.gz -C ./external/
@@ -317,8 +327,8 @@ if $install_panther ; then
 fi
 
 # Check SRA Toolkit installation
-if ( [ ! -e "./external/sratoolkit/bin/prefetch" ] &&
-     [ -e "./external/sratoolkit/bin/fasterq-dump" ] ); then
+if [ ! -e "./external/sratoolkit/bin/prefetch" ] &&
+   [ -e "./external/sratoolkit/bin/fasterq-dump" ]; then
 	packagesNotInstalled+=("SRA-Tools")
 fi
 
@@ -348,8 +358,8 @@ if [ ! -e "./external/trinityrnaseq/Trinity" ]; then
 fi
 
 # Check BLAST installation
-if ( [ ! -e "./external/ncbi-blast+/bin/blastx" ] ||
-     [ ! -e "./external/ncbi-blast+/bin/blastp" ] ); then
+if [ ! -e "./external/ncbi-blast+/bin/blastx" ] ||
+   [ ! -e "./external/ncbi-blast+/bin/blastp" ]; then
 	packagesNotInstalled+=("BLAST+")
 fi
 
@@ -369,8 +379,8 @@ if [ ! -e "./external/salmon/bin/salmon" ]; then
 fi
 
 # Check TransDecoder installation
-if ( [ ! -e "./external/TransDecoder/TransDecoder.LongOrfs" ] ||
-     [ ! -e "./external/TransDecoder/TransDecoder.Predict" ] ); then
+if [ ! -e "./external/TransDecoder/TransDecoder.LongOrfs" ] ||
+   [ ! -e "./external/TransDecoder/TransDecoder.Predict" ]; then
 	packagesNotInstalled+=("TransDecoder")
 fi
 
@@ -391,14 +401,14 @@ fi
 #========================================================================
 
 echo "Now building Semblans ..."
-mkdir ./bin/
+mkdir -p ./bin
 make
 
 # Determine if build was successful
-if ( [ ! -e "./bin/preprocess" ] ||
-     [ ! -e "./bin/assemble" ] ||
-     [ ! -e "./bin/postprocess" ] ||
-     [ ! -e "./bin/semblans" ] ); then
+if [ ! -e "./bin/preprocess" ] ||
+   [ ! -e "./bin/assemble" ] ||
+   [ ! -e "./bin/postprocess" ] ||
+   [ ! -e "./bin/semblans" ]; then
 	echo "ERROR: Semblans failed to build from source"
 	exit 1
 else