1 - For these tools, when you will unzip miRNA directory, 3 directories will be created under galaxy_dist/tools/ to house downloaded tools.
sm_miRNA_qual
sm_mirdeep2
sm_miRNA_annotations


2 - In the new directory, place the XML and any script file(s) which were contained in the archive.


3 - If the tool includes binaries, you'll need to copy them to a directory on your $PATH. If the tool depends on C binaries but does not come with them (only source), you'll need to compile the source first.

Tools which should be installed on your cluster : 
fastqc : FastQC v0.10.0
cutadapt : v1.0
bowtie version 0.12.8
bwa Version: 0.6.1-r104
miRDeep2 : "2.0.0.5"
samtools version: 0.1.18 (r982:295)

sed -i -e "s|/usr/local/bioinfo/bin/bwa|/path/to/your/bwa|" sm_mirdeep2/sm_bwa.pl

sed -i -e "s|/usr/local/bioinfo/bin/samtools|/path/to/your/samtools|" sm_mirdeep2/sm_bwa.pl

sed -i -e "s|/usr/local/bioinfo/bin/samtools|/path/to/your/samtools|" sm_mirdeep2/sm_miRNA_filtrer_aln.pl
 
sed -i -e "s|/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/sm_mirdeep2/mapper.pl|/path/to/mapper script|" sm_mirdeep2/sm_mapper.pl


sed -i -e "s|/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/sm_mirdeep2/miRDeep2.pl|/path/to/miRDeep2 script|" sm_mirdeep2/sm_mirdeep2core.pl

sed -i -e "s|:/usr/local/bioinfo/bin|/your/$ENV/path|" sm_mirdeep2/sm_mirdeep2core.pl


sed -i -e "s|/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/sm_miRNA_annotations/join.pl|/path/to/join script|" sm_miRNA_annotations/sm_join_matrice.pl

sed -i -e "s|/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/sm_miRNA_annotations/lists2venn.pl|/path/to/lists2venn script|" sm_miRNA_annotations/venn.pl

sed -i -e "s|/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/sm_miRNA_qual/fastqnr.pl|/path/to/fastqnr script|" sm_miRNA_qual/sm_miRNA_fastqnr.pl

sed -i -e "s|/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/sm_miRNA_qual/join.pl|/path/to/join script|" sm_miRNA_qual/sm_miRNA_join.pl

sed -i -e "s|/usr/local/bioinfo/src/python/current/bin/cutadapt|/path/to/cutadapt script|" sm_miRNA_qual/sm_miRNA_qual.pl

sed -i -e "s|/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/sm_miRNA_qual/matrix.pl|/path/to/matrix script|" sm_miRNA_qual/sm_miRNA_matrix.pl

sed -i -e "/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/sm_miRNA_qual/plot1.pl|/path/to/plot1 script|" sm_miRNA_qual/sm_miRNA_stats_qual.pl


sed -i -e "/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/sm_miRNA_qual/stat1_V2.pl|/path/to/stat1_V2 script|" sm_miRNA_qual/sm_miRNA_stats_qual.pl

No dependancies for miRNA tools.



4 - Add the tool to galaxy_dist/tool_conf.xml.

<section name="Qualite / Nettoyage / Mirdeep2 / Annotation" id="mirdeep2">
    <tool file="rgenetics/rgFastQC.xml" />
    <tool file="sm_miRNA_qual/sm_miRNA_qual.xml" />
    <tool file="sm_miRNA_qual/sm_miRNA_fastqnr.xml" />
    <tool file="sm_miRNA_qual/sm_miRNA_join.xml" />
    <tool file="sm_miRNA_qual/sm_miRNA_matrix.xml" />
    <tool file="sm_miRNA_qual/sm_miRNA_stats_qual.xml" />
    <tool file="sm_mirdeep2/sm_mapper.xml" />
    <tool file="sm_mirdeep2/sm_mirdeep2core.xml" />
    <tool file="sm_mirdeep2/sm_mirdeep2core_bed_to_fasta.xml" />
    <tool file="sm_mirdeep2/sm_bwa.xml" />
    <tool file="sm_miRNA_annotations/sm_miRNA_join_matrice.xml" />
    <tool file="sm_miRNA_annotations/sm_miRNA_venn.xml" />
</section> 

5 - Restart your Galaxy server process.


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