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| wiki:software:mb668 [2024/03/20 15:13] – keistc | wiki:software:mb668 [2024/03/20 15:20] (current) – keistc |
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| This class required numerous packages to download and compile. | This class required numerous packages to download and compile. |
| a list of software that we will need to run for the computing labs: | a list of software that we will need to run for the computing labs: |
| * R and Rscript Already installed in the docker image.\ | * R and Rscript Already installed in the docker image. |
| * [[https://github.com/BenLangmead/bowtie2|Bowtie2]] Click on tags and then download the latest version. Unzip the file and then cp the bowtie2* files into the hub bin folder. | * [[https://github.com/BenLangmead/bowtie2|Bowtie2]] Click on tags and then download the latest version. Unzip the file and then cp the bowtie2* files into the hub bin folder. |
| * [[https://github.com/samtools/samtools/releases/|SAMtools]] Download the source file. Then ./configure --prefix=/home/.hub_local, make, make install | * [[https://github.com/samtools/samtools/releases/|SAMtools]] Download the source file. Then ./configure --prefix=/home/.hub_local, make, make install |
| This will get the metabat1 and metabat2 compiled. But failed after that. Will see if the rest is needed. | This will get the metabat1 and metabat2 compiled. But failed after that. Will see if the rest is needed. |
| * [[https://github.com/Ecogenomics/CheckM/wiki/Installation|CheckM]] Follow link and use the pip3 install instructions using the hubpip command. Python packages numby, matplotlib are already installed. | * [[https://github.com/Ecogenomics/CheckM/wiki/Installation|CheckM]] Follow link and use the pip3 install instructions using the hubpip command. Python packages numby, matplotlib are already installed. |
| * [[https://github.com/broadinstitute/picard/releases|picard]] Download the latest version that will run with the version of Java on the hub. Version 2.75 worked on the current hub. Placed the jar file in the hub_data_share folder. To test run: java -jar picard.jar -h | * [[https://github.com/broadinstitute/picard/releases|picard]] Download the latest version that will run with the version of Java on the hub. Version 2.27.4 worked on the current hub. Placed the jar file in the hub_data_share folder. To test run: java -jar picard.jar -h |
