Adding additional deps to dockerfile

docker/sqanti3/Dockerfile

@@ -1,23 +1,23 @@
-# Base image for SQANTI3,
+# Base image for SQANTI3/v5.1.2,
 # uses Ubuntu Jammy (LTS)
 FROM ubuntu:22.04
 
 # Depedencies of SQANTI:
 #  - https://github.com/ConesaLab/SQANTI3/wiki/Dependencies-and-installation
 #  - https://github.com/ConesaLab/SQANTI3/blob/master/SQANTI3.conda_env.yml
 # Overview:
-#  - perl                      # apt-get, installs: 5.34.0-3
-#  - minimap2                  # apt-get, installs: 2.24
-#  - kallisto                  # apt-get, installs: 0.46.2
-#  - samtools                  # apt-get, installs: 1.13-4
-#  - STAR                      # from github, installs: 2.7.10b
-#  - uLTRA                     # from pypi: installs: 0.1
-#  - deSALT                    # from github: https://github.com/ydLiu-HIT/deSALT
-#  - bedtools                  # apt-get, installs: 2.30.0
-#  - gffread                   # apt-get, installs: 0.12.7-2
-#  - gmap                      # apt-get, installs: 2021-12-17+ds-1
-#  - seqtk                     # apt-get, installs: 1.3-2
-#  - R>=3.4                    # apt-get, installs: 4.1.2-1
+#  -+ perl                      # apt-get, installs: 5.34.0-3
+#  -+ minimap2                  # apt-get, installs: 2.24
+#  -+ kallisto                  # apt-get, installs: 0.46.2
+#  -+ samtools                  # apt-get, installs: 1.13-4
+#  -+ STAR                      # apt-get, installs: 2.7.10a
+#  -+ uLTRA                     # from pypi: installs: 0.1
+#  -+ deSALT                    # from github: https://github.com/ydLiu-HIT/deSALT
+#  -+ bedtools                  # apt-get, installs: 2.30.0
+#  -+ gffread                   # apt-get, installs: 0.12.7-2
+#  -+ gmap                      # apt-get, installs: 2021-12-17+ds-1
+#  -+ seqtk                     # apt-get, installs: 1.3-2
+#  -+ R>=3.4                    # apt-get, installs: 4.1.2-1
 #     @requires: noiseq        # from Bioconductor
 #     @requires: busparse      # from Bioconductor
 #     @requires: biocmanager   # from CRAN
@@ -47,22 +47,22 @@ FROM ubuntu:22.04
 #     @requires: stringr       # from CRAN
 #     @requires: tibble        # from CRAN
 #     @requires: tidyr         # from CRAN
-#  - python>3.7                # apt-get, installs: 3.10.4-0
-#     @requires: bx-python     # pip install from pypi
-#     @requires: biopython     # pip install from pypi
-#     @requires: bcbio-gff     # pip install from pypi 
-#     @requires: cDNA_Cupcake  # pip install from github
-#     @requires: Cython        # pip install from pypi 
-#     @requires: numpy         # pip install from pypi
-#     @requires: pysam         # pip install from pypi
-#     @requires: pybedtools    # pip install from pypi, needs bedtools
-#     @requires: psutil        # pip install from pypi
-#     @requires: pandas        # pip install from pypi
-#     @requires: scipy         # pip install from pypi
+#  -+ python>3.7                # apt-get, installs: 3.10.6-1
+#     @requires: bx-python      # pip install from pypi
+#     @requires: biopython      # pip install from pypi
+#     @requires: bcbio-gff      # pip install from pypi 
+#     @requires: cDNA_Cupcake   # pip install from github
+#     @requires: Cython         # pip install from pypi 
+#     @requires: numpy          # pip install from pypi
+#     @requires: pysam          # pip install from pypi
+#     @requires: pybedtools     # pip install from pypi, needs bedtools
+#     @requires: psutil         # pip install from pypi
+#     @requires: pandas         # pip install from pypi
+#     @requires: scipy          # pip install from pypi
 LABEL maintainer="Skyler Kuhn <[email protected]>" \
     base_image="ubuntu:22.04" \
     version="v0.1.0"   \
-    software="modr" \
+    software="sqanti3/v5.1.2" \
     about.summary="SQANTI3: Tool for the Quality Control of Long-Read Defined Transcriptomes" \
     about.home="https://github.com/ConesaLab/SQANTI3" \
     about.documentation="https://github.com/ConesaLab/SQANTI3/wiki/" \
@@ -85,15 +85,114 @@ RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime \
 # This section installs system packages 
 # required for your project. If you need 
 # extra system packages add them here.
+RUN apt-get update \
+    && apt-get -y upgrade \
+    && DEBIAN_FRONTEND=noninteractive apt-get install -y \
+        # bedtools/2.30.0
+        bedtools \
+        build-essential \
+        cmake \
+        cpanminus \
+        curl \
+        gawk \
+        # gffread/0.12.7
+        gffread \
+        git \
+        # gmap/2021-12-17
+        gmap \
+        gzip \
+        # kallisto/0.46.2
+        kallisto \
+        libcurl4-openssl-dev \
+        libssl-dev \
+        libxml2-dev \
+        locales \
+        # minimap2/2.24
+        minimap2 \
+        # perl/5.34.0-3
+        perl \
+        pkg-config \
+        # python/3.10.6
+        python3 \
+        python3-pip \
+        # R/4.1.2-1
+        r-base \
+        # STAR/2.7.10a
+        rna-star \
+        # samtools/1.13-4
+        samtools \
+        # seqtk/1.3-2
+        seqtk \
+        wget \
+        zlib1g-dev \
+    && apt-get clean && apt-get purge \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
+# Set the locale
+RUN localedef -i en_US -f UTF-8 en_US.UTF-8
+# Perl fix issue
+RUN cpanm FindBin Term::ReadLine
 
-############### INSTALL ################
-# Install any bioinformatics tools
-# available with apt-get on Ubuntu/22.04
+############### MANUAL ################
+# Install tools from src manually,
+# Installs deSALT/1.5.6 from GitHub:
+# https://github.com/ydLiu-HIT/deSALT/releases/tag/v1.5.6
+# This tool was created using an older
+# version of GCC that allowed multiple
+# definitions of global variables.
+# We are using GCC/10, which does not
+# allow multiple definitations. Adding
+# -Wl,--allow-multiple-definition
+# to the linker to fix this issue.
+RUN mkdir -p /opt2/desalt/1.5.6/ \
+    && wget https://github.com/ydLiu-HIT/deSALT/archive/refs/tags/v1.5.6.tar.gz -O /opt2/desalt/1.5.6/v1.5.6.tar.gz \
+    && tar -zvxf /opt2/desalt/1.5.6/v1.5.6.tar.gz -C /opt2/desalt/1.5.6/ \
+    && rm -f /opt2/desalt/1.5.6/v1.5.6.tar.gz \
+    && cd /opt2/desalt/1.5.6/deSALT-1.5.6/src/deBGA-master/ \
+    && make CFLAGS="-g -Wall -O2 -Wl,--allow-multiple-definition" \
+    && cd .. \
+    && make CFLAGS="-g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function -Wl,--allow-multiple-definition"
 
+ENV PATH="${PATH}:/opt2/desalt/1.5.6/deSALT-1.5.6/src"
+WORKDIR /opt2
 
-############### MANUAL ################
-# Install tools from src manually
+# Installs namfinder, requirement of
+# ultra-bioinformatics tool from pypi.
+RUN mkdir -p /opt2/namfinder/0.1.3/ \
+    && wget https://github.com/ksahlin/namfinder/archive/refs/tags/v0.1.3.tar.gz -O /opt2/namfinder/0.1.3/v0.1.3.tar.gz \
+    && tar -zvxf /opt2/namfinder/0.1.3/v0.1.3.tar.gz -C /opt2/namfinder/0.1.3/ \
+    && rm -f /opt2/namfinder/0.1.3/v0.1.3.tar.gz \
+    && cd /opt2/namfinder/0.1.3/namfinder-0.1.3/ \
+    # Build to be compatiable with most
+    # Intel x86 CPUs, should work with
+    # old hardware, i.e. sandybridge
+    && cmake -B build -DCMAKE_C_FLAGS="-msse4.2" -DCMAKE_CXX_FLAGS="-msse4.2" \
+    && make -j -C build
+
+ENV PATH="${PATH}:/opt2/namfinder/0.1.3/namfinder-0.1.3/build"
+WORKDIR /opt2
+
+############### INSTALL ################
+# Install any bioinformatics packages
+# available with pypi or CRAN/BioC
+RUN ln -sf /usr/bin/python3 /usr/bin/python
+RUN pip3 install --upgrade pip \
+    && pip3 install Cython \
+    && pip3 install bcbio-gff \
+    && pip3 install biopython \
+    && pip3 install bx-python \
+    && pip3 install matplotlib \
+    && pip3 install numpy \
+    && pip3 install pandas \
+    && pip3 install psutil \
+    && pip3 install pybedtools \
+    && pip3 install pysam \
+    && pip3 install scipy \
+    && pip3 install ultra-bioinformatics
+
+# !TODO: Install cDNA_Cupcake from Github
+# And install R packages, and finally
+# install SQANTI3/v5.1.2
 
 
 ################ POST #################