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orp-software [2019/10/25 18:38] – created aorthorp-software [2019/10/31 08:45] (current) – aorth
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 <code>$ module load orp/2.2.8 <code>$ module load orp/2.2.8
-$ </code>+$ /export/apps/orp/2.2.8/oyster.mk</code> 
 + 
 +Read [[https://oyster-river-protocol.readthedocs.io/en/latest/|the documentation]] to see more information about how to run Oyster River Protocol.
  
 ===== Installation ====== ===== Installation ======
-Notes from the sysadmin during installation:+Notes from the sysadmin during installation. First, create a chroot on the local filesystem to perform the installation.
  
 <code>$ mkdir -p /var/tmp/chroot/orp <code>$ mkdir -p /var/tmp/chroot/orp
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 $ sudo mount -t proc procfs /var/tmp/chroot/orp/proc $ sudo mount -t proc procfs /var/tmp/chroot/orp/proc
 $ sudo mount -t sysfs sysfs /var/tmp/chroot/orp/sys $ sudo mount -t sysfs sysfs /var/tmp/chroot/orp/sys
-$ sudo chroot /var/tmp/chroot/orp +$ sudo chroot /var/tmp/chroot/orp</code> 
-# Try to loosely follow instructions in the Dockerfile (download ORP tarball instead of cloning in git) + 
-# wget https://github.com/macmanes-lab/Oyster_River_Protocol/archive/2.2.8.tar.gz+Then, after entering the chroot, try to loosely follow the instructions in the Dockerfile and the Makefile until you get the orp virtual environment activated: 
 + 
 +<code># wget https://github.com/macmanes-lab/Oyster_River_Protocol/archive/2.2.8.tar.gz
 # tar xf 2.2.8.tar.gz # tar xf 2.2.8.tar.gz
 # mv Oyster_River_Protocol-2.2.8 /export/apps/orp/2.2.8 # mv Oyster_River_Protocol-2.2.8 /export/apps/orp/2.2.8
 # cd /export/apps/orp/2.2.8 # cd /export/apps/orp/2.2.8
-# Try to loosely follow instructions in the Makefile 
 # wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh # wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
 # bash Miniconda3-latest-Linux-x86_64.sh -b -p software/anaconda/install # bash Miniconda3-latest-Linux-x86_64.sh -b -p software/anaconda/install
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 # conda config --set sat_solver pycryptosat # conda config --set sat_solver pycryptosat
 # conda env create -f py37_env.yml python=3.7 # conda env create -f py37_env.yml python=3.7
-# conda activate orp+# conda activate orp</code> 
 + 
 +Set up a few extra pieces of software and download some data sets (see the Makefile):
  
-# Setup extra bits of data and software from Makefile +<code># git clone -b 2.0.1 https://github.com/bcgsc/transabyss.git software/transabyss
-# git clone -b 2.0.1 https://github.com/bcgsc/transabyss.git software/transabyss+
 # mkdir software/diamond # mkdir software/diamond
 # cd software/diamond && curl -LO ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz && gzip -d uniprot_sprot.fasta.gz # cd software/diamond && curl -LO ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz && gzip -d uniprot_sprot.fasta.gz
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 $ sudo mkdir -p /export/apps/orp/2.2.8 $ sudo mkdir -p /export/apps/orp/2.2.8
 $ sudo chown aorth /export/apps/orp/2.2.8 $ sudo chown aorth /export/apps/orp/2.2.8
-$ rsync -av /var/tmp/chroot/orp/export/apps/orp/2.2.8/ /export/apps/orp/2.2.8</code>+$ rsync -av /var/tmp/chroot/orp/export/apps/orp/2.2.8/ /export/apps/orp/2.2.8 
 +$ sudo chown -R root:root /export/apps/orp/2.2.8</code>
  
 Oyster River Protocol has dozens of dependencies and is essentially impossible to install without the use of [[https://conda.io/miniconda.html|Miniconda]]. My strategy is to install Conda somewhere globally and then use it to install Oyster River Protocol. Furthermore, I first installed orp/2.2.8 in a chroot on the local file system and then rsync'd it over to the network applications directory. This is MUCH faster. Oyster River Protocol has dozens of dependencies and is essentially impossible to install without the use of [[https://conda.io/miniconda.html|Miniconda]]. My strategy is to install Conda somewhere globally and then use it to install Oyster River Protocol. Furthermore, I first installed orp/2.2.8 in a chroot on the local file system and then rsync'd it over to the network applications directory. This is MUCH faster.
  
 To create the [[https://github.com/ilri/hpc-environment-modules/tree/master/orp|modulefile]] I compared the output ''env'' before and after loading the orp environment with Conda. To create the [[https://github.com/ilri/hpc-environment-modules/tree/master/orp|modulefile]] I compared the output ''env'' before and after loading the orp environment with Conda.
orp-software.1572028707.txt.gz · Last modified: by aorth