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Make clearer that the env vars are exectuables, not dirs #93

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May 27, 2016
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Make clearer that the env vars are exectuables, not dirs #93

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16 changes: 4 additions & 12 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ The environment variable is checked first and is used if it is set.
Otherwise ARIBA looks in your `$PATH` for the default name. This applies
to the following dependencies.

| Dependency | Default | Environment variable name |
| Dependency | Default executable | Environment variable name |
|----------------|------------------------|---------------------------|
| BCFtools | `bcftools` | `$ARIBA_BCFTOOLS` |
| Bowtie2 | `bowtie2` | `$ARIBA_BOWTIE2` |
Expand All @@ -63,18 +63,10 @@ to the following dependencies.
| SSPACE | `SSPACE_Basic_v2.0.pl` | `$ARIBA_SSPACE` |


For example, you could specify an exact version of Samtools using
(assuming BASH):

export ARIBA_SAMTOOLS=/path/to/samtools

The path need not be absolute. ARIBA looks for the value of the variable
in your $PATH. For example, suppose you have `samtools-0.1.19` and
`samtools-1.3` installed. You could use this:

export ARIBA_SAMTOOLS=samtools-1.3

For example, you could specify an exact version of a Samtools executable
(assuming BASH) that you compiled and downloaded in your home directory:

export ARIBA_SAMTOOLS=$HOME/samtools-1.2/samtools


Usage
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