![]() ![]() Instead of AppleClang, use a “proper” clang:.Install gappa via conda, instead of compiling on your own (it does not need OpenMp):.Here we provide two alternatives based on a discussion in gappa’s page, and you can read about it here. You need OpenMp, but it is a know issue that AppleClang on MacOSx does not work well with OpenMp. If you try to do the compilation with AppleClang on MacOSX it will probably fail. To install gappa you need make and cmake. To download Homebrew (assuming you don’t already have it) type: ruby -e "$(curl -fsSL )"Īssuming all that went okay go ahead and download the software you need to execute just the paprica-run.sh portion of paprica. These are no longer needed for paprica but I’ve left the Homebrew step in here because if you’re doing anything sciency with your computer you probably want a package manager, and I find wget to be a much more useful file fetching utility than curl. Older versions of paprica needed the programs pplacer and gappa, which had dependencies that could only be acquired for OSX for a package manager such as Homebrew. You should get a sensible error that is clearly seqmagick yelling at you and not your computer trying to find seqmagick. Seqmagick is a standalone program, not a module, so check the installation by typing: seqmagick If you get any error messages something somewhere is wrong. Open a shell, type “python3” and: import numpy In case you have conflicts with other Python installations, or some other mysterious problems, it’s a good idea to test things out at this point. Install some necessary Python modules, assuming you don’t already have them: pip3 install numpy Note that Python 3 must be callable on your system as “python3” which should be the default. If you already have a mainstream v3.0 Python distro going just make sure that the modules listed below are installed ( e.g., with conda install and not pip3). Therefore you need Python up and running on your system. The scripts that execute the pipeline are bash scripts, the scripts that do the actual work are Python. Paprica is 90 % an elaborate set of wrapper scripts for several core programs written by other groups. This tutorial assumes you’ve followed this advice, and that you are installing all the dependencies in your home directory. You might think, “but I’m the only user, so this makes more sense” or “but everyone in the lab wants program X, so I should install as root.” Don’t do it. ** IMPORTANT ** It is generally considered very poor practice to install anything in the root directory. This tutorial has been updated for the most recent version of paprica, and will not work for v0.6 or earlier. If you notice errors, inconsistencies, or omissions please leave a comment and I’ll be sure to correct them. Please note that this tutorial is a work in progress. If command line operations stress you out, and you haven’t dealt with a lot of weird bioinformatics program installs, use this tutorial. If you’re comfortable editing your PATH and installing things using bash you probably don’t need to follow this tutorial, just get the dependencies as indicated in the install instructions and linux_install.sh script. Inexperienced users should find it easy to work with, particularly thanks to its simplicity.The following is a paprica installation tutorial for novice users on Mac OSX (installation on Linux is quite a bit simpler). The bottom line is that Ultracopier is an advanced tool that comes with plenty of features. While copying, the files can be set to retain the original date and rights. Thus, you can select the language and have the program replace the default copy and move system from Windows. The program comes with an extensive “Options” area. ![]() Settings regarding file collisions and errors can be made as well. The task can be paused and resumed at any time and you can even skip certain files or quit the process altogether.īy default, the frame closes at the end of the process if there are no errors, but you can modify this option. The entire list of files can be viewed as well and the order in which these are copied can be modified. Once you launch the operation, you can view the entire size of the folder and of the file that is currently being moved. In order to do this, you are requested to define an input and output directory. Thus, you can copy, transfer or move any files to a location of your choice. The program has a simple interface that is quite easy to figure out, thanks to the intuitive layout. Ultracopier is a light tool that was designed to enable you to perform all these tasks with just a few clicks. Every time you decide to organize the files on your computer you are faced with countless hours spent copying, moving and transferring documents, photographs and entire folders to one area or another. ![]()
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