Add docker support to bowtie and bowtie2.

[heuermh]

No description provided.

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[heuermh]

The linuxbrew docker build for bowtie appears to not have pulled in a python dependency

17/10/27 11:56:02 INFO NewHadoopRDD: Input split: file://q.ifq:0+268
Unable to find image 'heuermh/bowtie:latest' locally
latest: Pulling from heuermh/bowtie
ae79f2514705: Already exists
5ad56d5fc149: Already exists
170e558760e8: Already exists
395460e233f5: Already exists
6f01dc62e444: Already exists
574a4adca268: Already exists
558cc6645fe6: Already exists
8fe33a780b44: Already exists
86915709e3f7: Already exists
ddb605284e34: Pulling fs layer
ddb605284e34: Verifying Checksum
ddb605284e34: Download complete
ddb605284e34: Pull complete
Digest: sha256:0297ae9dc5fb1d3e817c410d914cb068328e410a5f95079d68b2df69800656c4
Status: Downloaded newer image for heuermh/bowtie:latest
/usr/bin/env: 'python': No such file or directory
17/10/27 11:59:25 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
17/10/27 11:59:25 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
17/10/27 11:59:25 ERROR Utils: Aborting task
java.lang.RuntimeException: Piped command List(docker, run, --rm, heuermh/bowtie, bowtie, -S, q.fa, --12, -) exited with error code 127.
	at org.bdgenomics.adam.rdd.OutFormatterRunner.hasNext(OutFormatter.scala:37)

[heuermh]

Bowtie 2 works for me locally using docker with an additional --mount argument for the reference.

Support for --interleaved was added in bowtie version 1.2.1. Waiting on dockerhub for a new bowtie docker build to test.

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