![]() Gmhmme3=/work/GIF/software/programs/GeneMark-ES/4.32/gmes_petap/gmhmme3 #location of eukaryotic genemark executable Snap=/work/GIF/software/programs/snap//snap #location of snap executable RepeatMasker=/work/GIF/software/programs/repeatmasker/4.0.6/RepeatMasker #location of RepeatMasker executableĮxonerate=/work/GIF/software/programs/exonerate/2.2.0/bin/exonerate #location of exonerate executable Xdformat= #location of WUBLAST xdformat executableīlasta= #location of WUBLAST blasta executable ![]() Tblastx=/work/GIF/software/programs/ncbi-blast/2.2.28+/bin/tblastx #location of NCBI+ tblastx executableįormatdb= #location of NCBI formatdb executableīlastall= #location of NCBI blastall executable ![]() Makeblastdb=/work/GIF/software/programs/rmblast/2.2.28/bin/makeblastdb #location of NCBI+ makeblastdb executableīlastn=/work/GIF/software/programs/ncbi-blast/2.2.28+/bin/blastn #location of NCBI+ blastn executableīlastx=/work/GIF/software/programs/rmblast/2.2.28/bin/blastx #location of NCBI+ blastx executable #-Location of Executables Used by MAKER/EVALUATOR To ensure proper parsing of the files, make sure that there are no spaces between the equal sign and the path to the files. ![]() I will only use blastn, blastx, tblastx, repeatmasker, exonerate, snap, gmhmme3(GeneMark), and augustus. Maker_opts.ctl - This is the key control file that will be subject to change for each round of maker. Maker_bopts.ctl - This one controls the parameters of each program if you want to change the default settings. Maker_exe.ctl- This file points to the executable programs that we will be using. #Of course you can use maker to copy these files for you #Copy the 3 maker control files, which are essentially config files needed to run makerįor f in /work/GIF/remkv6/Purcell/Abalone/29_MakerP/02_MakerRun2/maker_* do cp $f. This includes the predicted transcripts and proteins from all genome assemblies in this clade. Download all transcriptional resources for the clade in which your species residesįor the soybean cyst nematode, that includes all publicly available resources for the Tylenchida. This leads us to the first step of finding all transcriptional and protein resources for the initial MAKER prediction. While there are multiple ways to run Maker, all tips and tutorials that I have run across have always done the maker annotation first, and then incorporated the other ab-initio predictors subsequently. Is there a specific order to run different predictors in Maker? Here is a Maker tutorial that gave me the idea to use BUSCO to train Augustus. There are a number of nice Maker tutorials that can found online. The “Genome Annotation and Curation Using MAKER and MAKER-P” publication has a list of example protocols that may be helpful and may add some detail to my choices below. This version of maker includes the addition of multiple gene ab-initio prediction tools as well as AED score support for gene models. This is the original publication for the MAKER2 gene prediction pipeline. This is the original MAKER publication, which details more about the general MAKER algorithm, when MAKER lacked all other gene predictors besides SNAP. I have outlined how to perform a gene annotation of the soybean cyst nematode ( Heterodera glycines) genome using Maker2. xvfb does not need to startup at boot time because the software uses xvfb-run which starts an isolated xvfb session for a specific executable.Tutorial of how to run Maker2 gene annotation pipeline See install_ubuntu for the typical installation of this. To fix this xvfb can be installed which is a lightweight virtual replacement for xserver. Headless servers typically do not have xserver installed. Snapgene server requires some X window system to generate SVG maps and make font measurements. The name "snapuser" can be changed too as long as the ss-start script is updated as well. The script also creates a group named "snapuser" but this can be changed by IT to aid file permissions when making file specific requests to the server. See bash script install_ubuntu for the command line to create the user. The installation assumes the name "snapuser". Snapgene server can run as a separate restricted system user. The server also makes use of python scripts that require the python zmq package to be installed. The snapgene-server executable is written in C++ and the libzmq.so.3 shared library is installed automatically into the executable directory. Snapgene server uses the zmq library for interprocess and intra-net communication within a server environment. See this link for information on how to install "ms core fonts" without using the keyboard. This can cause problems for automated installers. Note that the install scripts install "ms core fonts" which requires the user accept a license agreement interactively. See script $EXEDIR/install/install_ubuntu and install_fedora for the libraries and other changes required to run the server successfully.
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