Merge branch 'development' into 'master'

Add new packages to bioinformatis package and uncomment

See merge request !6

files/bioinformatics.yml

@@ -37,12 +37,13 @@ dependencies:
   - biom-format=2.1.7=py36h3010b51_1002
   - biopython=1.74=py36h516909a_0
   - blas=2.11=openblas
-  - blast=2.9.0=pl526h979a64d_3
+  - blast=2.9.0=pl526h3066fca_4
   - bleach=3.1.0=py_0
   - bokeh=1.3.1=py36_0
   - boost=1.68.0=py36h8619c78_1001
   - boost-cpp=1.68.0=h11c811c_1000
   - bowtie=1.2.0=py36_0
+  - bwa=0.7.17=hed695b0_6
   - bwidget=1.9.11=0
   - bz2file=0.98=py_0
   - bzip2=1.0.8=h516909a_1
@@ -69,12 +70,13 @@ dependencies:
   - entrypoints=0.3=py36_1000
   - expat=2.2.5=he1b5a44_1003
   - fastcluster=1.1.25=py36h637b7d7_1000
-  - fastqc=0.11.8=1
+  - fastqc=0.11.8=2
   - fasttree=2.1.10=0
   - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
   - fontconfig=2.13.1=he4413a7_1000
   - freetype=2.10.0=he983fc9_1
   - future=0.17.1=py36_1000
+  - gatk=3.7=py36_0
   - gcc_impl_linux-64=7.3.0=habb00fd_1
   - gcc_linux-64=7.3.0=h553295d_8
   - gettext=0.19.8.1=hc5be6a0_1002
@@ -95,16 +97,18 @@ dependencies:
   - harfbuzz=2.4.0=h37c48d4_1
   - hdf5=1.10.4=nompi_h3c11f04_1106
   - hdmedians=0.13=py36hc1659b7_1001
+  - htslib=1.9=ha228f0b_7
   - icu=58.2=hf484d3e_1000
   - idna=2.8=py36_1000
   - ijson=2.3=py_1
   - importlib_metadata=0.18=py36_0
-  - insilicoseq=1.4.3=py_0
+  - insilicoseq=1.4.5=py_0
   - ipykernel=5.1.1=py36h5ca1d4c_0
   - ipython=7.7.0=py36h5ca1d4c_0
   - ipython_genutils=0.2.0=py_1
   - ipywidgets=7.5.1=py_0
   - iqtree=1.6.11.1=he513fc3_0
+  - java-jdk=8.0.92=1
   - jedi=0.14.1=py36_0
   - jinja2=2.10.1=py_0
   - joblib=0.13.2=py_0
@@ -145,6 +149,7 @@ dependencies:
   - markupsafe=1.1.1=py36h14c3975_0
   - matplotlib=3.1.1=py36_0
   - matplotlib-base=3.1.1=py36hfd891ef_0
+  - mira=4.9.6=1
   - mistune=0.8.4=py36h14c3975_1000
   - more-itertools=7.2.0=py_0
   - msgpack-python=0.6.1=py36h6bb024c_0
@@ -156,13 +161,14 @@ dependencies:
   - networkx=2.3=py_0
   - nose=1.3.7=py36_1002
   - notebook=6.0.0=py36_0
-  - numpy=1.17.2=py36h95a1406_0
+  - numpy=1.17.3=py36h95a1406_0
   - olefile=0.46=py_0
+  - openblas=0.3.6=h6e990d7_6
   - openjdk=11.0.1=h46a85a0_1017
   - openmp=8.0.1=0
-  - openssl=1.1.1c=h516909a_0
+  - openssl=1.1.1d=h516909a_0
   - packaging=19.0=py_0
-  - pandas=0.24.2=py36hb3f55d8_0
+  - pandas=0.24.2=py36hb3f55d8_1
   - pandoc=2.7.3=0
   - pandocfilters=1.4.2=py_1
   - pango=1.40.14=he7ab937_1005
@@ -240,6 +246,7 @@ dependencies:
   - pillow=6.0.0=py36he7afcd5_0
   - pip=19.2.1=py36_0
   - pixman=0.38.0=h516909a_1003
+  - plink=1.90b6.12=heea4ae3_0
   - pluggy=0.12.0=py_0
   - prometheus_client=0.7.1=py_0
   - prompt_toolkit=2.0.9=py_0
@@ -343,13 +350,14 @@ dependencies:
   - raxml=8.2.12=h14c3975_1
   - readline=8.0=hf8c457e_0
   - requests=2.22.0=py36_1
+  - samtools=1.9=h10a08f8_12
   - scikit-bio=0.5.5=py36h3010b51_1000
   - scikit-learn=0.21.2=py36hcdab131_1
-  - scipy=1.3.1=py36h921218d_2
-  - seaborn=0.9.0=py_1
+  - scipy=1.3.2=py36h921218d_0
+  - seaborn=0.9.0=py_2
   - send2trash=1.5.0=py_0
   - setuptools=41.0.1=py36_0
-  - simlord=1.0.3=pyh24bf2e0_2
+  - simlord=1.0.3=py36h516909a_3
   - sina=1.6.0=hc7f9b0f_0
   - sip=4.19.8=py36hf484d3e_1000
   - six=1.12.0=py36_1000
@@ -367,6 +375,7 @@ dependencies:
   - tzlocal=2.0.0=py_0
   - unifrac=0.10.0=py36h6bb024c_1
   - urllib3=1.25.3=py36_0
+  - velvet=1.2.10=hed695b0_3
   - vsearch=2.7.0=1
   - wcwidth=0.1.7=py_1
   - webencodings=0.5.1=py_1
@@ -396,5 +405,4 @@ dependencies:
   - zipp=0.5.1=py_0
   - zlib=1.2.11=h516909a_1006
   - zstd=1.4.0=h3b9ef0a_0
-prefix: /opt/miniconda/envs/bioinformatics
-
+prefix: /opt/anaconda/envs/bioinformatics
\ No newline at end of file

manifests/environments.pp

@@ -49,17 +49,17 @@ class anaconda::environments {
     path    => ['/bin','/opt/anaconda/bin']
   }
   
-  #file { '/opt/envs/bioinformatics.yml':
-  #  ensure  => present,
-  #  source  => 'puppet:///modules/anaconda/bioinformatics.yml',
-  #  require => File['/opt/envs'],
-  #}
+  file { '/opt/envs/bioinformatics.yml':
+    ensure  => present,
+    source  => 'puppet:///modules/anaconda/bioinformatics.yml',
+    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',
-  #  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',
+    require => File['/opt/envs/bioinformatics.yml'],
+    path    => ['/bin','/opt/anaconda/bin']
+  }
 
 }