scampi2

Setup

Requirements

1. Python 2.7+
2. CMake

Easy installation

git clone https://github.com/ElofssonLab/scampi2
cd scampi2
./install.sh

After that, scampi2 will be installed in the folder bin

Separated installation

1. Clone the github repository
2. Install modhmm

• mkdir /tmp/build
• cd /tmp/build
• cmake -D CMAKE_INSTALL_PREFIX=/my/install/dir /this/source/dir
• make
• make install

3. Install cmdline

• mkdir /tmp/build
• cd /tmp/build
• cmake -D TARGETS="scampi;scampi-msa" -D CMAKE_PREFIX_PATH=/path/to/modhmm -D CMAKE_INSTALL_PREFIX=/my/install/dir /this/source/dir
• make
• make install

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Usage

Scampi-Single:

    ./SCAMPI_run.pl \<input_fasta\> \<output_file\>

• <input_fasta> can contain one or more fasta entries

For example:

bin/scampi/SCAMPI_run.pl test/4seq.fasta test/4seq.out

Scampi-MSA:

    ./run_SCAMPI_multi.pl \<input_fasta\> \<output_file\> \<blast_dir\> \<blast_db\>

• <input_fasta> can contain only one (!) fasta entry

For example (suppose you have blastpgp installed at /usr/bin and blast database at /data/blastdb/uniref90.fasta):

bin/scampi-msa/run_SCAMPI_multi.pl test/1seq.fasta test/1seq.scampi-msa.out /usr /data/blastdb/uniref90.fasta