This page was last updated on Friday, 15-Nov-2019 08:20:52 CST

Installation notes for DISCOVAR version 52488

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Docker Container Installation

1. $ sudo apt-get install docker.io
2. $ sudo docker pull vera/discovardenovo
3. Example from web page:
   $ docker run -d --name ddn1 -v $(pwd):/ddn vera/discovardenovo READS=*fastq.gz NUM_THREADS=24 OUT_DIR=ddn
   -d, --detach Detached mode: run the container in the background and print the new container ID.
   --name Assign a name to the container
   -v|--volume[=[[HOST-DIR:]CONTAINER-DIR[:OPTIONS]]] Create a bind mount. If you specify, -v /HOST-DIR:/CONTAINER-DIR, Docker bind mounts /HOST-DIR in the host to /CONTAINER-DIR in the Docker container. If 'HOST-DIR' is omitted, Docker automatically creates the new volume on the host.

Prerequisites

• g++
• GMP library
• SAMtools
• graphviz
• Picard

Abandoned Local Installation

1. $ ver="52488"
2. $ cd /programinstallers/
3. $ wget -N ftp://ftp.broadinstitute.org/pub/crd/Discovar/latest_source_code/discovar-$ver.tar.gz
4. $ tar -zxvf discovar-$ver.tar.gz<
5. $ cd discovar-$ver
6. $ mkdir /usr/local/bin/discovar
7. $ ./configure --prefix=/usr/local/bin/discovar
8. $ make all
   …
   error: ‘memcpy’ was not declared in this scope
   …
9. I found a container at
   https://hub.docker.com/r/vera/discovardenovo/