From c11e5fbd7599173b7e64e8de43eee646c0acfe94 Mon Sep 17 00:00:00 2001 From: martinghunt Date: Fri, 27 May 2016 10:01:06 +0000 Subject: [PATCH 1/6] Update dependencies --- README.md | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 435d72a3..8212eea8 100644 --- a/README.md +++ b/README.md @@ -11,16 +11,15 @@ Installation ------------ ARIBA has the following dependencies, which need to be installed: - * [python3] [Python3] version >= 3.4 + * [Python3] [python] version >= 3.4 * [r] [R] version >= 2.14.0 - * [ape] [ape] version >= 3.1 + * The R package [ape] [ape] version >= 3.1 * [bowtie2] [Bowtie2] version >= 2.1.0 * [cd-hit] [cdhit] version >= 4.6 * [samtools and bcftools] [samtools] version >= 1.2 * [MUMmer] [mummer] version >= 3.23 - * Either [SPAdes] [spades] version >= 3.5.0 or [Velvet] [velvet] version >= 1.2.07 - (SPAdes is recommended) - * [python2] [Python2] version >= 2.7 (if SPAdes is used, Python2 is also required) + * [SPAdes] [spades] version >= 3.5.0 + * [Python2] [python] version >= 2.7 (SPAdes needs python2) ARIBA has the following optional dependencies. If they are installed, @@ -61,9 +60,8 @@ Build status: [![Build Status](https://travis-ci.org/sanger-pathogens/ariba.svg? [samtools]: http://www.htslib.org/ [spades]: http://bioinf.spbau.ru/spades [sspace]: http://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE - [velvet]: http://www.ebi.ac.uk/~zerbino/velvet/ [ape]: https://cran.r-project.org/web/packages/ape/index.html [r]: https://www.r-project.org/ - [python3]: https://www.python.org/ + [python]: https://www.python.org/ From 6625ef1ebc1aa2d12e19a46947d1a07a97498ba0 Mon Sep 17 00:00:00 2001 From: martinghunt Date: Fri, 27 May 2016 10:05:18 +0000 Subject: [PATCH 2/6] Fix all the links --- README.md | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index 8212eea8..ece567c4 100644 --- a/README.md +++ b/README.md @@ -11,22 +11,22 @@ Installation ------------ ARIBA has the following dependencies, which need to be installed: - * [Python3] [python] version >= 3.4 - * [r] [R] version >= 2.14.0 - * The R package [ape] [ape] version >= 3.1 - * [bowtie2] [Bowtie2] version >= 2.1.0 - * [cd-hit] [cdhit] version >= 4.6 - * [samtools and bcftools] [samtools] version >= 1.2 - * [MUMmer] [mummer] version >= 3.23 - * [SPAdes] [spades] version >= 3.5.0 - * [Python2] [python] version >= 2.7 (SPAdes needs python2) + * [Python3][python] version >= 3.4 + * [R][r] version >= 2.14.0 + * The R package [ape][ape] version >= 3.1 + * [bowtie2][Bowtie2] version >= 2.1.0 + * [cd-hit][cdhit] version >= 4.6 + * [samtools and bcftools][samtools] version >= 1.2 + * [MUMmer][mummer] version >= 3.23 + * [SPAdes][spades] version >= 3.5.0 + * [Python2][python] version >= 2.7 (SPAdes needs python2) ARIBA has the following optional dependencies. If they are installed, they will be used. Otherwise scaffolding and gap filling will be skipped. - * [SSPACE-basic scaffolder] [sspace] - * [GapFiller] [gapfiller] + * [SSPACE-basic scaffolder][sspace] + * [GapFiller][gapfiller] Once the dependencies are installed, install ARIBA using pip: @@ -45,7 +45,7 @@ If the tests all pass, install: Usage ----- -Please read the [ARIBA wiki page] [ARIBA wiki] for usage instructions. +Please read the [ARIBA wiki page][ARIBA wiki] for usage instructions. From 4f3a67a4e7702a391e079c9d6479c5af0183559d Mon Sep 17 00:00:00 2001 From: martinghunt Date: Fri, 27 May 2016 10:25:08 +0000 Subject: [PATCH 3/6] Add env vars description --- README.md | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/README.md b/README.md index ece567c4..ba19fc4a 100644 --- a/README.md +++ b/README.md @@ -42,6 +42,41 @@ If the tests all pass, install: python3 setup.py install +### Dependencies and environment variables + +By default, ARIBA will look for the dependencies in your `$PATH`, using +the names in the table below. This behaviour can be overridden and +point ARIBA to a specific program using environment variables. +The environment variable is checked first and is used if it is set. +Otherwise ARIBA looks in your `$PATH` for the default name. This applies +to the following dependencies. + +| Dependency | Default | Environment variable name | +|----------------|------------------------|---------------------------| +| BCFtools | `bcftools` | `$ARIBA_BCFTOOLS` | +| Bowtie2 | `bowtie2` | `$ARIBA_BOWTIE2` | +| CD-HIT | `cd-hit-est` | `$ARIBA_CDHIT` | +| GapFiller | `GapFiller.pl` | `$ARIBA_GAPFILLER` | +| R | `Rscript` | `$ARIBA_R` | +| Samtools | `samtools` | `$ARIBA_SAMTOOLS` | +| SPAdes | `spades.py` | `$ARIBA_SPADES` | +| SSPACE | `SSPACE_Basic_v2.0.pl` | `$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 + + + + Usage ----- From aafa881befdf9007e7de02e374751a067424f8b9 Mon Sep 17 00:00:00 2001 From: martinghunt Date: Fri, 27 May 2016 10:27:01 +0000 Subject: [PATCH 4/6] Consistent tool names --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index ba19fc4a..7a37e3f9 100644 --- a/README.md +++ b/README.md @@ -14,9 +14,9 @@ ARIBA has the following dependencies, which need to be installed: * [Python3][python] version >= 3.4 * [R][r] version >= 2.14.0 * The R package [ape][ape] version >= 3.1 - * [bowtie2][Bowtie2] version >= 2.1.0 - * [cd-hit][cdhit] version >= 4.6 - * [samtools and bcftools][samtools] version >= 1.2 + * [Bowtie2][bowtie2] version >= 2.1.0 + * [CD-HIT][cdhit] version >= 4.6 + * [Samtools and BCFtools][samtools] version >= 1.2 * [MUMmer][mummer] version >= 3.23 * [SPAdes][spades] version >= 3.5.0 * [Python2][python] version >= 2.7 (SPAdes needs python2) From 05f354eab51c2c304a85c2dd101435af68e05e48 Mon Sep 17 00:00:00 2001 From: martinghunt Date: Fri, 27 May 2016 10:28:02 +0000 Subject: [PATCH 5/6] Delete space in link --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 7a37e3f9..697c2ac6 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ ARIBA Antibiotic Resistance Identification By Assembly -For how to use ARIBA, please see the [ARIBA wiki page] [ARIBA wiki]. +For how to use ARIBA, please see the [ARIBA wiki page][ARIBA wiki]. From 787cabb03f236e489b6a3342d15b59774be5cce8 Mon Sep 17 00:00:00 2001 From: martinghunt Date: Fri, 27 May 2016 10:34:10 +0000 Subject: [PATCH 6/6] Version bump 1.0.0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 1da40e65..ccc1607a 100644 --- a/setup.py +++ b/setup.py @@ -7,7 +7,7 @@ setup( name='ariba', - version='0.6.0', + version='1.0.0', description='ARIBA: Antibiotic Resistance Identification By Assembly', packages = find_packages(), package_data={'ariba': ['test_run_data/*']},