update singularity recipes

Author: cokelaer

Singularity

@@ -12,22 +12,6 @@ OSVersion: xenial
     apt-get install -y wget
     apt-get install -y bzip2
     apt-get install -y vim
-    #apt-get install -y libgl1-mesa-glx  # will be required by pyqt
-    #apt-get install -y fontconfig # for sequanix/qt fonts otherwise no text in menus
-
-    # for fastqc
-    #apt-get install -y libxrender1
-    #apt-get install -y libxtst6
-    #apt-get install -y libxi6
-
-    # for sequanix (Qt plugin) otherwise libxcb missing
-    #apt-get install -y libsm-dev
-    #apt-get install -y libxcomposite-dev
-
-    # This is a large data set again. When using the container a sroot, sequanix
-    # looks good but in normal mode, the menu is blank...and this seems to solve
-    # the issue
-    apt-get install -y libgnomeui-0
 
     # install anaconda
     if [ ! -d /usr/local/anaconda ]; then
@@ -45,7 +29,6 @@ OSVersion: xenial
     export PATH=$PATH:/usr/local/anaconda/bin
     conda update conda
 
-
     conda config --add channels r
     conda config --add channels defaults
     conda config --add channels conda-forge
@@ -54,11 +37,6 @@ OSVersion: xenial
     # The main packages for sequana:
     conda install --file https://raw.githubusercontent.com/CancerRxGene/gdsctools/master/requirements.txt
 
-    # external tools
-
-    # Let us save some space
-    conda clean --packages -y
-
     # Let us save some space
     conda clean --packages -y
 

doc/installation.rst

@@ -8,7 +8,6 @@ Installation
 .. note:: For those insterested, as from Oct 11 2017, we provide a Signularity container. 
 
 
-
 You know **bioconda**, then you can install **GDSCTools** as follows::
 
 
@@ -27,8 +26,7 @@ Install conda executable
 
 In practice, we do use `Anaconda <https://conda.readthedocs.io/>`_ . We
 recommend to
-install **conda** executable via the manual installer (`download
-<https//continuum.io/downloads>_`). 
+install **conda** executable via the manual installer (`download <https//continuum.io/downloads>_`). 
 You may have the choice
 between Python 2 and 3. We recommend to choose a Python version 3.
 
@@ -180,4 +178,3 @@ Then, inside the container, install or fix the problem and type exit to save the
 container.
 
 
-