Skip to content
Permalink
Browse files

Update manual reflecting recent conda updates

  • Loading branch information...
lmrodriguezr committed Aug 25, 2019
1 parent b365517 commit dd124adf47a1c58ca74fdc8bfca7ee538d1a2f22
Showing with 22 additions and 21 deletions.
  1. +1 −2 manual/part2/requirements.md
  2. +20 −18 manual/part2/requirements/conda.md
  3. +1 −1 manual/summary.md
@@ -9,12 +9,11 @@ please continue these instructions.
MiGA has a relatively long list of requirements, but most of them are easy to
install. Find your system below and follow the instructions using:

* [Anaconda or Miniconda](requirements/conda.md),
* [`apt-get`](requirements/apt-get.md),
* [Homebrew or Linuxbrew](requirements/brew.md),
* [Anaconda or Miniconda](requirements/conda.md),
* [Installing from source](requirements/source.md).

In addition, you will also need the [MyTaxa utils](requirements/mytaxa.md)
in order to activate the [MyTaxa](../part5/workflow.md#mytaxa) and
[MyTaxa Scan](../part5/workflow.md#mytaxa-scan) steps (optional).

@@ -11,8 +11,8 @@ Now that you have Conda, activate it. If you want to create a separate clean
environment (optional) you can simply execute:

```bash
conda create -n miga
conda activate miga
conda create -y -n miga
source activate miga
```

It's strongly recommended to activate conda in the `~/.miga_modules`:
@@ -21,28 +21,31 @@ It's strongly recommended to activate conda in the `~/.miga_modules`:
# Tell MiGA to always activate conda:
echo 'eval "$(conda shell.bash hook)"' >> ~/.miga_modules
# Tell MiGA to activate the proper conda environment:
echo 'conda activate miga' >> ~/.miga_modules
echo 'source activate miga' >> ~/.miga_modules
```

Next, install the requirements:

```bash
conda install -y ruby r-base sqlite
conda install -y -c bioconda \
blast hmmer bedtools prodigal idba mcl barrnap \
fastqc solexaqa diamond krona fastani
conda install -y -c faircloth-lab scythe
conda install -y -c anaconda sqlite r-base
conda install -y -c conda-forge ruby=2.4.5
conda install -y -c conda-forge -c bioconda -c faircloth-lab \
scythe blast hmmer bedtools prodigal idba mcl barrnap \
fastqc diamond krona fastani solexaqa
```

Finally, conda's Ruby [is broken](https://github.com/ContinuumIO/anaconda-issues/issues/9863),
so we'll apply a quick patch to allow native gem installations:
**Note for MacOS users:**
> The current recipe for SolexaQA++ only supports
> Linux.
> However, a precompiled SolexaQA++ binary for MacOS can be obtained directly
> from the developers
> [here](https://downloads.sourceforge.net/project/solexaqa/src/SolexaQA++_v3.1.7.1.zip).
> Simply remove `solexaqa` from the list above, and download that binary
> manually.
```bash
cd $(gem environment gemdir)
cd ../../$(basename $PWD)/$(gem environment platform | perl -pe 's/.*://')
mv rbconfig.rb rbconfig.rb.bu
perl -pe 's/\/\S*?\/_build_env\/bin\///g' rbconfig.rb.bu > rbconfig.rb
```
**Note for Linux users:**
> In some environments you'll also need gfortran installed in order to compile
> some R packages: `conda install gfortran_linux-64`
## R packages

@@ -52,12 +55,11 @@ will install one package here to make sure everything is properly initialized.
```bash
R
install.packages('enveomics.R', repos = 'http://cran.rstudio.com/')
q()
q('no')
```

## MyTaxa utils

If you want to activate the [MyTaxa](../part5/workflow.md#mytaxa) and
[MyTaxa Scan](../part5/workflow.md#mytaxa-scan) steps, follow the instructions
to install the [MyTaxa Utils](mytaxa.md).

@@ -7,9 +7,9 @@
* [Definitions](glossary.md)
* [Part II: Getting started](part2.md)
* [Requirements](part2/requirements.md)
* [Using Conda](part2/requirements/conda.md)
* [Using apt-get](part2/requirements/apt-get.md)
* [Using Homebrew](part2/requirements/brew.md)
* [Using Conda](part2/requirements/conda.md)
* [Installing from source](part2/requirements/source.md)
* [MyTaxa Utils](part2/requirements/mytaxa.md)
* [Installation](part2/installation.md)

0 comments on commit dd124ad

Please sign in to comment.
You can’t perform that action at this time.