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In case you run into trouble compiling or testing\n+the LSST stack please install your compiler in anaconda:\n+\n+conda install gcc\n+\n+\n+* Create a directory for the PFS-DRP repositories:\n+\n+mkdir ~/stella-git\n+cd ~/stella-git\n+\n+* Clone the relevant git repositories:\n+\n+git clone https://github.com/Subaru-PFS/drp_stella.git\n+git clone https://github.com/Subaru-PFS/drp_stella_data.git\n+git clone https://github.com/Subaru-PFS/obs_pfs.git\n+\n+\n+* Install a newer version of eigen:\n+\n+eups distrib install eigen 3.2.5.lsst2\n+\n+\n+* Declare the git repositories in Linux (replace <Linux64> with <DarwinX86> for Mac OS X):\n+\n+eups declare obs_pfs 1.0 -c -f Linux64 -r ~/stella-git/obs_pfs\n+eups declare drp_stella_data 1.0 -c -f Linux64 -r ~/stella-git/drp_stella_data\n+eups declare drp_stella 1.0 -c -f Linux64 -r ~/stella-git/drp_stella\n+\n+\n+* Setup the pipeline. As obs_pfs and drp_stella_data are required packages they are set up automatically:\n+\n+setup drp_stella 1.0 -v\n+\n+During this step the environment variables $DRP_STELLA_DIR, $DRP_STELLA_DATA_DIR, and $OBS_PFS_DIR are automatically \n+created as well:\n+\n+echo $DRP_STELLA_DIR\n+\n+should show you:\n+\n+~/stella-git/drp_stella\n+\n+\n+* Build the pipeline:\n+\n+cd drp_stella\n+scons opt=3 -j8\n+\n+\n+* Create the defects database (done during compilation of the code):\n+\n+cd ../obs_pfs\n+scons opt=3 -j8\n+\n+\n+* Now for using the pipeline. Raw test data are in $DRP_STELLA_DATA_DIR/tests/data/raw/ (3 Biases, 3 Darks, 1 Flat, 1 Arc). \n+First we need to create a directory (actually 2) where we want to store pipeline outputs. \n+Let's assume you have a directory ~/spectra and do everything related to spectra there:\n+\n+mkdir ~/spectra/PFS\n+mkdir ~/spectra/PFS/CALIB\n+\n+\n+* Configuration parameters can be passed to the pipeline task either on the command line or in a config file \n+(e.g. $OBS_PFS_DIR/config/pfs/ingest.py, see following example). You can list all possible configuration parameters by \n+appending a \"--show config\" to the parameter list.\n+To ingest the raw images:\n+\n+cd ~/spectra\n+ingestImages.py PFS $DRP_STELLA_DATA_DIR/tests/data/raw/*.fits --output=PFS --mode=link -C $OBS_PFS_DIR/config/pfs/ingest.py\n+\n+\n+* You can now inspect the created SQL database with e.g. sqlitebrowser (http://sqlitebrowser.org/).","path":"doc/install.text","position":87,"original_position":87,"commit_id":"3c9f4cdd21a49d887a1980fed72e8cc736f3bbb6","original_commit_id":"3c9f4cdd21a49d887a1980fed72e8cc736f3bbb6","user":{"login":"jdswinbank","id":460854,"avatar_url":"https://avatars.githubusercontent.com/u/460854?v=3","gravatar_id":"","url":"https://api.github.com/users/jdswinbank","html_url":"https://github.com/jdswinbank","followers_url":"https://api.github.com/users/jdswinbank/followers","following_url":"https://api.github.com/users/jdswinbank/following{/other_user}","gists_url":"https://api.github.com/users/jdswinbank/gists{/gist_id}","starred_url":"https://api.github.com/users/jdswinbank/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jdswinbank/subscriptions","organizations_url":"https://api.github.com/users/jdswinbank/orgs","repos_url":"https://api.github.com/users/jdswinbank/repos","events_url":"https://api.github.com/users/jdswinbank/events{/privacy}","received_events_url":"https://api.github.com/users/jdswinbank/received_events","type":"User","site_admin":false},"body":"...or by just running `sqlite3`, which is more likely to be available. 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