# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
	. /etc/bashrc
fi

# User specific environment
if ! [[ "$PATH" =~ "$HOME/.local/bin:$HOME/bin:" ]]
then
    PATH="$HOME/.local/bin:$HOME/bin:$PATH"
fi
export PATH

# Uncomment the following line if you don't like systemctl's auto-paging feature:
# export SYSTEMD_PAGER=

# User specific aliases and functions
if [ -d ~/.bashrc.d ]; then
	for rc in ~/.bashrc.d/*; do
		if [ -f "$rc" ]; then
			. "$rc"
		fi
	done
fi

unset rc

PS1='\[\e[1;35;1m\][\u@\h \W]\$ \[\e[00m\]'
alias lh='ls -lh'
alias les='less -S'
alias del='gvfs-trash'

PATH=/opt/sysoft/Python-3.11.4/bin/:$PATH
PATH=/opt/sysoft/Python-2.7.18/bin/:$PATH
PATH=/opt/sysoft/R-4.0.2/bin/:$PATH
PATH=/opt/sysoft/jdk-20.0.1/bin:$PATH
PATH=$PATH:/opt/sysoft/jre1.8.0_371/bin
PATH=$PATH:/home/train/.aspera/connect/bin/
PATH=$PATH:/opt/biosoft/sratoolkit/bin/
PATH=$PATH:/opt/biosoft/FastQC/
PATH=/opt/biosoft/jellyfish-2.3.0/bin:$PATH
PATH=$PATH:/opt/biosoft/idba-1.1.3/bin/
PATH=$PATH:/opt/biosoft/canu-2.2/build/bin/
PATH=$PATH:/opt/biosoft/hifiasm-0.19.5/
PATH=$PATH:/opt/biosoft/minimap2-2.26
PATH=$PATH:/opt/biosoft/lastz-1.04.22/bin
PATH=$PATH:/opt/biosoft/rmblast-2.14.0/bin
PATH=$PATH:/opt/biosoft/RepeatMasker-4.1.5
PATH=$PATH:/opt/biosoft/mafft/bin/
PATH=$PATH:/opt/biosoft/RepeatModeler-2.0.4
PATH=$PATH:/opt/biosoft/Misa_Primer3/
PATH=$PATH:/opt/biosoft/primer3-2.6.1/src/
PATH=$PATH:/opt/biosoft/infernal-1.1.4/bin
PATH=$PATH:/opt/biosoft/tRNAscan-SE-2.0/bin/
PATH=$PATH:/opt/biosoft/tRNAscan-SE-1.3.1/bin/
export PERL5LIB=$PERL5LIB:/opt/biosoft/tRNAscan-SE-1.3.1/bin/
PATH=$PATH:/opt/biosoft/bowtie-1.3.1-linux-x86_64/
PATH=$PATH:/opt/biosoft/bowtie2-2.5.1-linux-x86_64/
PATH=$PATH:/opt/biosoft/bwa-0.7.17/
PATH=$PATH:/opt/biosoft/samtools-1.17/bin/
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/biosoft/htslib-1.17/lib/
export C_INCLUDE_PATH=$C_INCLUDE_PATH:/opt/biosoft/htslib-1.17/include/
PATH=$PATH:/opt/biosoft/htslib-1.17/bin/
PATH=$PATH:/opt/biosoft/hisat2-2.1.0/
PATH=$PATH:/opt/biosoft/gatk-4.4.0.0/
PATH=$PATH:/opt/biosoft/Trinity-v2.15.1/
PATH=$PATH:/opt/biosoft/salmon-latest_linux_x86_64/bin/
PATH=$PATH:/opt/biosoft/RSEM-1.3.3/
PATH=$PATH:/opt/biosoft/kallisto
PATH=$PATH:/opt/biosoft/TransDecoder-v5.5.0/
PATH=/opt/biosoft/hmmer-3.3.2/bin/:$PATH
PATH=$PATH:/opt/biosoft/cufflinks-2.2.1.Linux_x86_64/
PATH=$PATH:/opt/biosoft/stringtie-2.2.1.Linux_x86_64/
PATH=$PATH:/opt/biosoft/gmap-2017-11-15/bin/
PATH=$PATH:/opt/biosoft/pblat-2.5.1/
PATH=$PATH:/opt/biosoft/fasta-36.3.8g/bin/
PATH=$PATH:/opt/biosoft/blast-2.2.26/bin/
PATH=$PATH:/opt/biosoft/PASApipeline.v2.5.3/bin/
PATH=$PATH:/opt/sysoft/lighttpd-1.4.54/sbin/
export LD_LIBRARY_PATH=/opt/biosoft/boost_1_82_0/lib:$LD_LIBRARY_PATH
export C_INCLUDE_PATH=/opt/biosoft/boost_1_82_0/include:$C_INCLUDE_PATH
export LD_LIBRARY_PATH=/opt/sysoft/lp_solve_5.5/lpsolve55/bin/ux64:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/opt/sysoft/mysql++-3.3.0/lib:$LD_LIBRARY_PATH
PATH=$PATH:/opt/biosoft/Augustus-3.5.0/bin/
PATH=$PATH:/opt/biosoft/Augustus-3.5.0/scripts/
export AUGUSTUS_CONFIG_PATH=/opt/biosoft/Augustus-3.5.0/config/
PATH=$PATH:/opt/biosoft/wise2.4.1/src/bin/
PATH=$PATH:/opt/biosoft/geta-2.6.1/bin/
export WISECONFIGDIR=/opt/biosoft/wise2.4.1/wisecfg/
PATH=$PATH:/opt/biosoft/exonerate-2.2.0-x86_64/bin/
PATH=$PATH:/opt/biosoft/gmes_linux_64_4/
PATH=$PATH:/opt/biosoft/snap
PATH=$PATH:/opt/biosoft/BRAKER-3.0.3/scripts/
PATH=$PATH:/opt/biosoft/bedtools2/bin/
PATH=$PATH:/opt/biosoft/gth-1.7.3-Linux_x86_64-64bit/bin/
PATH=$PATH:/opt/biosoft/bbmap/
PATH=$PATH:/opt/biosoft/metaeuk/bin/
PATH=$PATH:/opt/biosoft/Prodigal-2.6.3/
PATH=/opt/biosoft/busco-5.4.7/bin:$PATH
export BUSCO_CONFIG_FILE=/opt/biosoft/busco-5.4.7/config/config.ini
PATH=$PATH:/opt/biosoft/SpliceGrapher-0.2.7/scripts/
PATH=$PATH:/opt/biosoft/gms2_linux_64//
PATH=$PATH:/opt/biosoft/tbl2asn/
PATH=$PATH:/opt/biosoft/circos-0.69-6/bin/
PATH=$PATH:/opt/biosoft/IGV_Linux_2.16.1/
PATH=$PATH:/opt/biosoft/ncbi-blast-2.14.0+/bin
PATH=$PATH:/opt/biosoft/diamond-2.1.8/bin
PATH=$PATH:/opt/biosoft/go_class/bin/
PATH=$PATH:/opt/biosoft/signalp-5.0/bin
PATH=$PATH:/opt/biosoft/tmhmm-2.0c/bin/
PATH=$PATH:/opt/biosoft/OrthoFinder-2.5.5/
PATH=$PATH:/opt/biosoft/Gblocks_0.91b/
PATH=$PATH:/opt/biosoft/FastTree
PATH=$PATH:/opt/biosoft/RAxML-8.2.12/
PATH=$PATH:/opt/biosoft/paml4.9i/bin
PATH=$PATH:/opt/biosoft/CAFE-5.1.0/bin/
PATH=$PATH:/opt/biosoft/MCScanX/
PATH=$PATH:/opt/biosoft/mummer-4.0.0rc1/bin/
PATH=$PATH:/opt/biosoft/mauve_2.4.0/