Merge pull request #20 from B-UMMI/gbs_types

v2.3

.gitignore

@@ -1,5 +1,5 @@
 # mpmachado_stuff - file with different mpmachado stuffs
-mpmachado_stuff.*
+mpmachado_stuff*
 
 # Samtools fasta indexing
 *.fai

Docker/Dockerfile

@@ -1,37 +1,38 @@
-FROM ubuntu:16.04
-MAINTAINER Miguel Machado <mpmachado@medicina.ulisboa.pt>
-LABEL version="2.2-02"
+FROM continuumio/miniconda3:4.8.2-alpine
+LABEL version="2.3-dev-2021-03"
 
-WORKDIR /NGStools/
+# -- Dependencies ---
 
-RUN apt-get update
+RUN /opt/conda/bin/conda install -y -c bioconda blast=2.10.1 && \
+    /opt/conda/bin/pip install setuptools && \
+    /opt/conda/bin/conda clean -y --all
 
-# -- General Dependencies ---
-RUN apt-get install -y wget git python python3 python3-pip && \
-    pip3 install setuptools
+ENV PATH="/opt/conda/bin:${PATH}"
 
 # -- seq_typing Dependencies ---
-# --- Blast+ ---
-RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7.1/ncbi-blast-2.7.1+-x64-linux.tar.gz && \
-    tar -xf ncbi-blast-2.7.1+-x64-linux.tar.gz && \
-    rm ncbi-blast-2.7.1+-x64-linux.tar.gz
-ENV PATH="/NGStools/ncbi-blast-2.7.1+/bin:${PATH}"
+
+WORKDIR /NGStools/
+
+USER root
+
+RUN apk add bash git libstdc++
+
 # --- ReMatCh ---
+# TODO: remove checkout
 RUN git clone https://github.com/B-UMMI/ReMatCh.git && \
     cd ReMatCh && \
-    # git checkout bowtie_algo && \
+    git checkout dev && \
     python3 setup.py install && \
     cd /NGStools
 
 # -- seq_typing --
+
+# TODO: remove checkout
 RUN git clone https://github.com/B-UMMI/seq_typing.git && \
     cd seq_typing && \
-    # git checkout bowtie_index && \
+    git checkout gbs_types && \
     python3 setup.py install
 
-# -- Clean --
-RUN pip3 uninstall setuptools && \
-    apt-get remove -y python3-pip && \
-    apt-get autoclean -y
+ENV PATH="/NGStools/ReMatCh/ReMatCh/src/samtools-1.3.1/bin:/NGStools/ReMatCh/ReMatCh/src/bcftools-1.3.1/bin:/NGStools/ReMatCh/ReMatCh/src/bowtie2-2.2.9:${PATH}"
 
 WORKDIR /data/

Docker/README.md

@@ -14,7 +14,7 @@ Within this image you can find:
 - Python v2.7.12 and v3.5.2
 - [Blast+](https://blast.ncbi.nlm.nih.gov/Blast.cgi) v2.7.1
 - [ReMatCh](https://github.com/B-UMMI/ReMatCh) v4.0.1
-- [seq_typing](https://github.com/B-UMMI/seq_typing) v2.2
+- [seq_typing](https://github.com/B-UMMI/seq_typing) v2.3
 
 
 ### Using play-with-docker
@@ -24,25 +24,25 @@ Within [play-with-docker](http://labs.play-with-docker.com/) webpage click on **
 will open with a big counter on the upper left corner. Click on **+ add new instance** and a terminal like instance should be generated on the right. On
 this terminal you can load this docker image as follows:
 
-`docker pull ummidock/seq_typing:2.2-01`
+`docker pull ummidock/seq_typing:2.3-01`
 
 #### Build this docker on your local machine
 
 For this, docker needs to be installed on your machine. Instructions for this can be found [here](https://docs.docker.com/engine/installation/).
 
 ##### Using DockerHub (automated build image)
 
-`docker pull ummidock/seq_typing:2.2-01`
+`docker pull ummidock/seq_typing:2.3-01`
 
 ##### Using GitHub (build docker image)
 
 1) `git clone https://github.com/B-UMMI/seq_typing.git`  
-2) `docker build -t ummidock/seq_typing:2.2-01 ./seq_typing/Docker/`
+2) `docker build -t ummidock/seq_typing:2.3-01 ./seq_typing/Docker/`
 
 ### Run (using automated build image)
 Example of _Haemophilus influenzae_ serotyping using reads and provided references sequences (adapted from [here](../README.md#reads)).
 ````bash
-docker run --rm -u $(id -u):$(id -g) -it -v /local/folder/fastq_data:/data/ ummidock/seq_typing:2.2-01 \
+docker run --rm -u $(id -u):$(id -g) -it -v /local/folder/fastq_data:/data/ ummidock/seq_typing:2.3-01 \
     seq_typing.py reads --org Haemophilus influenzae \
                         --fastq /data/sample_1.fq.gz /data/sample_2.fq.gz \
                         --outdir /data/sample_out/ \
@@ -57,13 +57,13 @@ For more examples on how to run **seq_typing** without a Docker container see ge
 
 ```bash
 # Get Docker image
-udocker pull ummidock/seq_typing:2.2-01
+udocker pull ummidock/seq_typing:2.3-01
 
 # Create container (only needed to be done once)
-udocker create --name=seq_typing_2-2_01 ummidock/seq_typing:2.2-01
+udocker create --name=seq_typing_2-3_01 ummidock/seq_typing:2.3-01
 
 # Run seq_typing
-udocker run --user $(id -u):$(id -g) -v /local/folder/fastq_data:/data/ seq_typing_2-2_01 \
+udocker run --user $(id -u):$(id -g) -v /local/folder/fastq_data:/data/ seq_typing_2-3_01 \
     seq_typing.py reads --org Haemophilus influenzae \
                         --fastq /data/sample_1.fq.gz /data/sample_2.fq.gz \
                         --outdir /data/sample_out/ \