Practical Haplotype Graph Docker images pull down and creating a simple example database

Question

[지용]

When I used the "docker pull maizegenetics/phg", There are still layers that come out waiting at download done. so, I think unsuccessfully docker images down.

because, when I get to Step 0-D(Test the Docker by creating and running an example) I get the following error:

**[pool-1-thread-1] ERROR net.maizegenetics.plugindef.AbstractPlugin - getBufferedReader: Error getting reader for: /root/temp/phgSmallSeq/postgresDocker/Dockerfile

/root/temp/phgSmallSeq/postgresDocker/Dockerfile (No such file or directory) **

I have questions:

1. why occurred this error?

1-1. unsuccessfully docker images down?

1-2. wrong config.txt file?

host=myserverip:myport\n
user=sqlite\n
password=sqlite\n
DB=/tempFileDir/outputDir/phgTestDB_mapq48.db
DBtype=sqlite

2. when did my step wrong?

 docker pull maizegenetics/phg

 docker run -idt -v /hpvol/user/jysong/phg/:/phg/ -w /phg
 maizegenetics/phg /bin/bash

 docker exec -it dockername bash

 /tassel-5-standalone/run_pipeline.pl -debug -Xmx1G 
-CreateSmallGenomesPlugin -baseDir /phg/basedir -geneLength 3000 -interGeneLength 3500 -numberOfGenes 10 -endPlugin > /hpvol/user/jysong/phg/smallGenomes_log.txt

3. Postgres is necessary?

4. any advice, please.

Thank you very much for your time.

Answer 1

[lcj34]

I'm not sure why you got the message relating to the postgres docker file not being found. No, postgres is not required. At which step did that occur?

I ran the test commands from the wiki and did not see the same error as you did. But there were other errors. The example is old and needs work to explain which files must be manually created at each step. I am able to get this partially running but there are still problems that need addressing. I will add this to our list of PHG things to fix. I'm sorry this isn't working now.

[지용]

Thanks for the answer to the question.

1-1. unsuccessfully docker images down?

There are layers where the 'waiting' phrase remains even though the Docker image has been downloaded. Is this not a problem?