Merge branch 'scriptstobash' into 'master'

...ormance_reports/blast_with_allinea_performance_reports.md

...rmance_reports/lammps_with_allinea_performance_reports.md

...rformance_reports/ray_with_allinea_performance_reports.md

...ools/alignment_tools/blast/create_local_blast_database.md

...cs_tools/alignment_tools/blast/running_blast_alignment.md

...app_specific/bioinformatics_tools/alignment_tools/blat.md

...p_specific/bioinformatics_tools/alignment_tools/bowtie.md

..._specific/bioinformatics_tools/alignment_tools/bowtie2.md

...rmatics_tools/alignment_tools/bwa/running_bwa_commands.md

...fic/bioinformatics_tools/alignment_tools/clustal_omega.md

...ic/bioinformatics_tools/alignment_tools/tophat_tophat2.md

...tions/app_specific/bioinformatics_tools/biodata_module.md

..._manipulation_tools/bamtools/running_bamtools_commands.md

..._manipulation_tools/samtools/running_samtools_commands.md

...ioinformatics_tools/data_manipulation_tools/sratoolkit.md

...ific/bioinformatics_tools/de_novo_assembly_tools/oases.md

...ecific/bioinformatics_tools/de_novo_assembly_tools/ray.md

...ioinformatics_tools/de_novo_assembly_tools/soapdenovo2.md

...sembly_tools/trinity/running_trinity_in_multiple_steps.md

...embly_tools/velvet/running_velvet_with_paired_end_data.md