Merge branch 'development' into 'master'

Merge development to master

See merge request !17

files/bioinformatics.yml

 name: bioinformatics
 channels:
   - faircloth-lab
-  - qiime2/label/r2019.7
-  - anaconda
-  - conda-forge
   - bioconda
+  - conda-forge
+  - anaconda
   - defaults
 dependencies:
   - _libgcc_mutex=0.1=main
@@ -51,13 +50,14 @@ dependencies:
   - bwidget=1.9.11=0
   - bz2file=0.98=py_0
   - bzip2=1.0.8=h516909a_1
-  - ca-certificates=2019.11.28=hecc5488_0
+  - ca-certificates=2020.6.24=0
   - cachecontrol=0.12.5=py_0
   - cairo=1.16.0=h18b612c_1001
-  - certifi=2019.11.28=py36_0
+  - certifi=2020.6.20=py36_0
   - cffi=1.12.3=py36h8022711_0
   - chardet=3.0.4=py36_1003
   - click=7.0=py_0
+  - clustalo=1.2.3=0
   - cryptography=2.7=py36h72c5cf5_0
   - curl=7.65.3=hf8cf82a_0
   - cutadapt=2.4=py36h14c3975_0
@@ -69,6 +69,7 @@ dependencies:
   - defusedxml=0.5.0=py_1
   - dinopy=2.0.1=py36h6bb024c_1
   - dnaio=0.3=py36h14c3975_1
+  - emboss=6.6.0=he06d7ca_1
   - emperor=1.0.0b19=py36_0
   - entrez-direct=11.0=pl526_0
   - entrypoints=0.3=py36_1000
@@ -132,6 +133,7 @@ dependencies:
   - libffi=3.2.1=he1b5a44_1006
   - libgcc=7.2.0=h69d50b8_2
   - libgcc-ng=9.1.0=hdf63c60_0
+  - libgd=2.2.5=hceca4fd_3
   - libgfortran-ng=7.3.0=hdf63c60_0
   - libiconv=1.15=h516909a_1005
   - liblapack=3.8.0=11_openblas
@@ -143,6 +145,7 @@ dependencies:
   - libstdcxx-ng=9.1.0=hdf63c60_0
   - libtiff=4.0.10=h57b8799_1003
   - libuuid=2.32.1=h14c3975_1000
+  - libwebp=1.0.1=h8e7db2f_0
   - libxcb=1.13=h14c3975_1002
   - libxml2=2.9.9=h13577e0_2
   - llvm-openmp=8.0.1=hc9558a2_0
@@ -170,7 +173,7 @@ dependencies:
   - openblas=0.3.6=h6e990d7_6
   - openjdk=11.0.1=h46a85a0_1017
   - openmp=8.0.1=0
-  - openssl=1.1.1d=h516909a_0
+  - openssl=1.1.1g=h7b6447c_0
   - packaging=19.0=py_0
   - pandas=0.24.2=py36hb3f55d8_1
   - pandoc=2.7.3=0
@@ -273,30 +276,6 @@ dependencies:
   - pytz=2019.2=py_0
   - pyyaml=5.1.2=py36h516909a_0
   - pyzmq=18.0.2=py36h1768529_2
-  - q2-alignment=2019.7.0=py36_0
-  - q2-composition=2019.7.0=py36_0
-  - q2-cutadapt=2019.7.0=py36_0
-  - q2-dada2=2019.7.0=py36_0
-  - q2-deblur=2019.7.0=py36_0
-  - q2-demux=2019.7.0=py36_0
-  - q2-diversity=2019.7.0=py36_0
-  - q2-emperor=2019.7.0=py36_0
-  - q2-feature-classifier=2019.7.0=py36_0
-  - q2-feature-table=2019.7.0=py36_0
-  - q2-fragment-insertion=2019.7.0=py36_0
-  - q2-gneiss=2019.7.0=py36_0
-  - q2-longitudinal=2019.7.0=py36_0
-  - q2-metadata=2019.7.0=py36_0
-  - q2-phylogeny=2019.7.0=py36_0
-  - q2-quality-control=2019.7.0=py36_0
-  - q2-quality-filter=2019.7.0=py36_0
-  - q2-sample-classifier=2019.7.1=py36_0
-  - q2-taxa=2019.7.0=py36_0
-  - q2-types=2019.7.0=py36_0
-  - q2-vsearch=2019.7.0=py36_0
-  - q2cli=2019.7.0=py36_0
-  - q2templates=2019.7.0=py36_0
-  - qiime2=2019.7.0=py36_0
   - qt=5.9.7=h52cfd70_2
   - r-assertthat=0.2.1=r35h6115d3f_1
   - r-backports=1.1.4=r35hcdcec82_1
@@ -370,6 +349,7 @@ dependencies:
   - sortmerna=2.0=he860b03_4
   - spades=3.13.1=h2d02072_2
   - sqlite=3.29.0=hcee41ef_1
+  - sra-tools=2.8.0=0
   - statsmodels=0.10.1=py36hc1659b7_0
   - tbb=2019.7=hc9558a2_0
   - terminado=0.8.2=py36_0
@@ -411,4 +391,5 @@ dependencies:
   - zipp=0.5.1=py_0
   - zlib=1.2.11=h516909a_1006
   - zstd=1.4.0=h3b9ef0a_0
-prefix: /opt/anaconda/envs/bioinformatics
+prefix: /local-machine/.conda/envs/bioinformatics
\ No newline at end of file
+

manifests/environments.pp

@@ -55,12 +55,12 @@ class anaconda::environments {
     require => File['/opt/envs'],
   }
 
-  #exec { 'setupbioinformatics':
-  #  unless  => "conda env list | grep -q '/opt/anaconda/envs/bioinformatics'",
-  #  command => 'conda env create -f /opt/envs/bioinformatics.yml',
-  #  environment => ["SHELL=/bin/bash"],
-  #  require => File['/opt/envs/bioinformatics.yml'],
-  #  path    => ['/bin','/opt/anaconda/bin']
-  #}
+  exec { 'setupbioinformatics':
+    unless  => "conda env list | grep -q '/opt/anaconda/envs/bioinformatics'",
+    command => 'conda env create -f /opt/envs/bioinformatics.yml',
+    environment => ["SHELL=/bin/bash"],
+    require => File['/opt/envs/bioinformatics.yml'],
+    path    => ['/bin','/opt/anaconda/bin']
+  }
 
 }