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I want to use the scripts but formatdb is no longer available on new blast because is an older blast version. Docker is a way to package sripts and applications with their dependencies in order that they can still running (https://www.docker.com/). On this docker file I packaged Bioperl, blast2 (older blast) and your scripts. To use it you need to install docker as explained on ` https://docs.docker.com/engine/installation/linux/ Once docker is installed can be used in multiple applicactions. After docker installation genomic fluidity app must be build: `docker build -t genomicfluidity . ` and run `docker run -t -i -v /mygenomesDirectory:/usr/src/fluidity genomicfluidity /bin/bash` And can be used. It works fine for me on NCBI genomes, and may be useful for other people who has docker. Unfortunately it doesn't work fine with RAST genomes gbk format.
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Can you explain in more detail as to how to do this. I am on a linux server that has docker preinstalled. So when I run: docker build -t genomicfluidity It just says ""docker build" requires exactly 1 argument. Usage: docker build [OPTIONS] PATH | URL | - Build an image from a Dockerfile" Am I missing a step? Do I need to download the file from somewhere? |
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Hello |
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When I run: docker build -t genomicfluidity . it just hangs. I am definitely in the folder with the Dockerfile. Could it just be taking a long time? |
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Well, it takes a long time, but what you could do, is trying to comment on several lines of the docker file, just to test if it is working. Dockerfile is sequentially read, so you can add a number sign (#) at the beginning of every line except the first one, and see what happened. If you cant send an email and perhaps we can try a zoom meeting. I also think that with the docker file perhaps server admin can also help you? |
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I am actually trying to run this directly on my mac through the docker desktop, and now get the following error when I attempt to build: #6 3.778 Entering bioperl-live-master
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2 participants
I want to use the scripts but formatdb is no longer available on new blast because is an older blast version. Docker is a way to package sripts and applications with their dependencies in order that they can still running (https://www.docker.com/). On this docker file I packaged Bioperl, blast2 (older blast) and your scripts. To use it you need to install docker as explained on
https://docs.docker.com/engine/installation/linux/ Once docker is installed can be used in multiple applicactions. After docker installation genomic fluidity app must be build:docker build -t genomicfluidity .and rundocker run -t -i -v /mygenomesDirectory:/usr/src/fluidity genomicfluidity /bin/bash`And can be used.
It works fine for me on NCBI genomes, and may be useful for other people who has docker.
Unfortunately it doesn't work fine with RAST genomes gbk format.