The soykb from dockerpedia

soykb's Introduction

Soybean-Workflow

How to run

First, you must run the container.

docker run --detach \
        --interactive \
        --tty \
        --name soybean \
        dockerpedia/soykb:latest

Next, you must enter the container. You can confirm that you are inside of the container by the prompt

root@docker-instance:~# docker exec -ti -u workflow:workflow soybean bash
workflow@a0f861e6fbc4:~$ 
workflow@a0f861e6fbc4:~$ cd soykb/
workflow@a0f861e6fbc4:~/soykb$ ./workflow-generator --exec-env distributed

And follow the instructions of Pegasus

Troubleshooting

Workflow has hardware requirements, you can edit these requirements on the file named: workflow-generator.

        mem_mb = mem_gb * 1000
        self.addProfile(Profile(Namespace.CONDOR,
                                key="request_cpus",
                                value=str(cores)))
        self.addProfile(Profile(Namespace.PEGASUS,
                                key="pmc_request_cpus",
                                value=str(cores)))
        self.addProfile(Profile(Namespace.CONDOR,
                                key="request_memory",
                                value=str(mem_mb)))
        self.addProfile(Profile(Namespace.PEGASUS,
                                key="pmc_request_memory",
                                value=str(mem_mb)))
        self.addProfile(Profile(Namespace.CONDOR,
                                key="request_disk",
                                value=str(20*1024*1024)))

If the hardware does not meet the requirements your work will be idle. You can use the command condor_q -better-analyze. Here is an example:

workflow@a0f861e6fbc4:~/soykb$ condor_q -better-analyze
The Requirements expression for your job is:

    ( isUndefined(GLIDEIN_Entry_Name) ) && ( TARGET.Arch == "X86_64" ) &&
    ( TARGET.OpSys == "LINUX" ) && ( TARGET.Disk >= RequestDisk ) &&
    ( TARGET.Memory >= RequestMemory ) && ( TARGET.Cpus >= RequestCpus ) &&
    ( TARGET.HasFileTransfer )

Your job defines the following attributes:

    RequestCpus = 2
    RequestDisk = 20971520
    RequestMemory = 3000

The Requirements expression for your job reduces to these conditions:

         Slots
Step    Matched  Condition
-----  --------  ---------
[0]           2  isUndefined(GLIDEIN_Entry_Name)
[1]           2  TARGET.Arch == "X86_64"
[3]           2  TARGET.OpSys == "LINUX"
[5]           2  TARGET.Disk >= RequestDisk
[7]           2  TARGET.Memory >= RequestMemory
[9]           0  TARGET.Cpus >= RequestCpus

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soykb's Issues

Permission issues

Hi! I cannot execute the workflow with the provided commands:

daniel@gin-nuest:~$ docker exec -ti -u workflow:workflow soybean bash
workflow@1d974218c269:~$ whoami
workflow
workflow@1d974218c269:~$ cd soykb/
workflow@1d974218c269:~/soykb$ ls     
AutoADAG.py   README.md  inputs-fastq.txt       inputs-ref.txt  workflow-generator
AutoADAG.pyc  conf       inputs-fastq.txt.orig  software        wrappers
workflow@1d974218c269:~/soykb$ ./workflow-generator --exec-env distributed
bash: ./workflow-generator: Permission denied
workflow@1d974218c269:~/soykb$

There is no local user "workflow" on my machine, so "-u workflow" should suffice?

The file workflow-generator is owned by root:

workflow@1d974218c269:~/soykb$ ll
total 148
drwxr-xr-x 1 workflow workflow  4096 Nov 10 23:34 ./
drwxr-xr-x 1 workflow workflow  4096 Apr 18 13:15 ../
-rw-r--r-- 1 workflow workflow  6148 Apr  1  2015 .DS_Store
-rw-r--r-- 1 workflow workflow    82 Apr  1  2015 ._.DS_Store
-rw-r--r-- 1 workflow workflow   239 Jan 30  2015 ._.gitignore
-rw-r--r-- 1 workflow workflow   239 Jan 30  2015 ._.project
-rw-r--r-- 1 workflow workflow   239 Jan 30  2015 ._.pydevproject
-rw-r--r-- 1 workflow workflow   239 Jan 30  2015 ._AutoADAG.py
-rw-r--r-- 1 workflow workflow   239 Jan 30  2015 ._AutoADAG.pyc
-rw-r--r-- 1 workflow workflow   239 Jan 30  2015 ._README.md
-rwxr-xr-x 1 workflow workflow   239 Feb 19  2015 ._conf*
-rw-r--r-- 1 workflow workflow   290 Feb 20  2015 ._inputs-fastq.txt
-rw-r--r-- 1 workflow workflow   290 Feb 20  2015 ._inputs-fastq.txt.orig
-rw-r--r-- 1 workflow workflow   239 Jan 30  2015 ._inputs-ref.txt
-rwxr-xr-x 1 workflow workflow   239 Jan 30  2015 ._workflow-generator*
-rw-r--r-- 1 workflow workflow    15 Jan 30  2015 .gitignore
-rw-r--r-- 1 workflow workflow   370 Jan 30  2015 .project
-rw-r--r-- 1 workflow workflow   302 Jan 30  2015 .pydevproject
-rw-r--r-- 1 workflow workflow  2971 Jan 30  2015 AutoADAG.py
-rw-r--r-- 1 workflow workflow  2456 Jan 30  2015 AutoADAG.pyc
-rw-r--r-- 1 workflow workflow  2071 Jan 30  2015 README.md
drwxr-xr-x 4 workflow workflow  4096 Nov 10 23:34 conf/
-rw-r--r-- 1 workflow workflow   120 Feb 20  2015 inputs-fastq.txt
-rw-r--r-- 1 workflow workflow  3100 Feb 20  2015 inputs-fastq.txt.orig
-rw-r--r-- 1 workflow workflow   482 Jan 30  2015 inputs-ref.txt
drwxr-xr-x 7 workflow workflow  4096 Jan 30  2015 software/
-rw-r--r-- 1 root     root     33898 Nov 10 23:32 workflow-generator
drwxr-xr-x 2 workflow workflow  4096 Nov 10 23:34 wrappers/

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