TRM-23751

- Download latest rules from ARBA instead of SAAS
- Use ARBA rules instead of SAAS rules in unifire-workflow.sh

README.md

 # UniFIRE Project
 
 UniFIRE (The UniProt Functional annotation Inference Rule Engine) is an engine to execute rules in the UniProt Rule
- Markup Language (URML) format. It can be used to execute the UniProt annotation rules (UniRule and SAAS).
+ Markup Language (URML) format. It can be used to execute the UniProt annotation rules (UniRule and ARBA).
 
 This project is a work in progress, open for collaboration.
 
@@ -90,12 +90,12 @@ This is a simple example, which shows how to use the UniFIRE Docker image to run
 ```
 This command will use as input the file samples/proteins.fasta which is in multi-FASTA format with the header in
  the format as described above. It will run the whole UniFIRE workflow to predict functional annotations from UniRule
- and SAAS rules. The resulting functional predictions will be written into these files in the current working
+ and ARBA rules. The resulting functional predictions will be written into these files in the current working
  directory:
 ```
 predictions_unirule.out
 predictions_unirule-pirsr.out
-predictions_saas.out
+predictions_arba.out
 ```
 
 ### Runtime
@@ -133,7 +133,7 @@ $ <Path to UniFIRE parent folder>/build.sh
 
 Depending on the speed of your internet connection, it will take a few minutes to download all dependencies through 
 maven. You will require in total ~500 MB disk space in UniFIRE folder and in your local maven cache. The script also 
-downloads the latest UniRule, UniRule-PIRSR and SAAS rules in URML format and UniRule template
+downloads the latest UniRule, UniRule-PIRSR and ARBA rules in URML format and UniRule template
 alignments in fact XML format from EBI FTP into samples/ folder. Additionally it downloads data neccassary to run
 UniRule-PIRSR rules from https://proteininformationresource.org/pirsr/pirsr_data_latest.tar.gz and places them
 underneath the folder samples/pirsr_data. 
@@ -151,9 +151,10 @@ $ ./distribution/bin/unifire.sh -r samples/unirule-urml-latest.xml -i samples/in
 *Note: To be able to predict the UniRule positional annotations, a template file is provided (`samples/unirule-templates-2018_05.xml`) (optional.)*
 <br/>
 
-**Example with SAAS rules & Fact XML input:**
+**Example with ARBA rules & Fact XML input:**
 ``` bash
-$ ./distribution/bin/unifire.sh -r samples/saas-urml-latest.xml -i samples/input_facts.xml -s XML -o output_saas_annotations.csv
+$ ./distribution/bin/unifire.sh -r samples/arba-urml-latest.xml -i samples/input_facts.xml -s XML -o
+ output_arba_annotations.csv
 ```
 <br/>
 
@@ -195,7 +196,7 @@ usage: unifire -i <INPUT_FILE> -o <OUTPUT_FILE> -r <RULE_URML_FILE> [-f <OUTPUT_
      -o,--output <OUTPUT_FILE>              Output file (path) containing predictions in the format
                                             specified in the -f option.
      -r,--rules <RULE_URML_FILE>            Rule base file (path) provided by UniProt (e.g UniRule
-                                            or SAAS) (format: URML).
+                                            or ARBA) (format: URML).
      -f,--output-format <OUTPUT_FORMAT>     Output file format. Supported formats are:
                                             - TSV (Tab-Separated Values)
                                             - XML (URML Fact XML)

build.sh

@@ -41,7 +41,7 @@ popd > /dev/null
 
 
 echo "Downloading rule urml files..."
-for file in saas-urml-latest.xml unirule-urml-latest.xml unirule-templates-latest.xml unirule.pirsr-urml-latest.xml;
+for file in arba-urml-latest.xml unirule-urml-latest.xml unirule-templates-latest.xml unirule.pirsr-urml-latest.xml;
 do
     backup_file ${SCRIPT_DIR}/samples/${file}
     wget ${FTP_SRC}/${file} -O ${SCRIPT_DIR}/samples/${file}

distribution/src/main/java/uk/ac/ebi/uniprot/unifire/UniFireApp.java

@@ -51,7 +51,7 @@ public class UniFireApp {
         Options options = new Options();
 
         Option ruleFileOption = Option.builder("r").longOpt("rules").hasArg().argName("RULE_URML_FILE")
-                .desc("Rule base file (path) provided by UniProt (e.g UniRule or SAAS) (format: URML).")
+                .desc("Rule base file (path) provided by UniProt (e.g UniRule or ARBA) (format: URML).")
                 .type(File.class).required().build();
         Option inputFileOption = Option.builder("i").longOpt("input").hasArg().argName("INPUT_FILE")
                 .desc("Input file (path) containing the proteins to annotate and required data, in the format specified by the -s option.")

docker/bin/run_unifire_docker.sh

@@ -40,7 +40,7 @@ outdir=""
 workdir=""
 cleanworkdir=0
 docker_version="2020.3"
-predictionfiles="predictions_unirule.out predictions_saas.out predictions_unirule-pirsr.out"
+predictionfiles="predictions_unirule.out predictions_arba.out predictions_unirule-pirsr.out"
 
 while getopts "i:o:w:c:v:" optionName
 do

docker/scripts/download-interproscan.sh

@@ -25,13 +25,13 @@ DOWNLOAD_FOLDER="/opt/download"
 mkdir -p ${DOWNLOAD_FOLDER}
 cd ${DOWNLOAD_FOLDER}
 echo "Downloading InterProScan..."
-wget -q ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.44-79.0/interproscan-5.44-79.0-64-bit.tar.gz
+wget -q ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.45-80.0/interproscan-5.45-80.0-64-bit.tar.gz
 echo "Done."
-wget -q ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.44-79.0/interproscan-5.44-79.0-64-bit.tar.gz.md5
+wget -q ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.45-80.0/interproscan-5.45-80.0-64-bit.tar.gz.md5
 
-ipr_check=`md5sum -c interproscan-5.44-79.0-64-bit.tar.gz.md5`
+ipr_check=`md5sum -c interproscan-5.45-80.0-64-bit.tar.gz.md5`
 
-if [[ ${ipr_check} != "interproscan-5.44-79.0-64-bit.tar.gz: OK" ]]
+if [[ ${ipr_check} != "interproscan-5.45-80.0-64-bit.tar.gz: OK" ]]
 then
 	exit 11
 fi
@@ -39,7 +39,7 @@ fi
 mkdir -p ${ROOT_FOLDER}
 cd ${ROOT_FOLDER}
 echo "Extracting InterProScan..."
-tar -pxzf ${DOWNLOAD_FOLDER}/interproscan-5.44-79.0-64-bit.tar.gz
+tar -pxzf ${DOWNLOAD_FOLDER}/interproscan-5.45-80.0-64-bit.tar.gz
 echo "Done."
 
 cd ${DOWNLOAD_FOLDER}
@@ -54,13 +54,13 @@ then
 	exit 12
 fi
 
-cd ${ROOT_FOLDER}/interproscan-5.44-79.0/data
+cd ${ROOT_FOLDER}/interproscan-5.45-80.0/data
 echo "Extracting Panther data..."
 tar -pxzf ${DOWNLOAD_FOLDER}/panther-data-14.1.tar.gz
 echo "Done."
 
 # Clean up tar to reduce the size of the image
-rm -f ${DOWNLOAD_FOLDER}/interproscan-5.44-79.0-64-bit.tar.gz
-rm -f ${DOWNLOAD_FOLDER}/interproscan-5.44-79.0-64-bit.tar.gz.md5
+rm -f ${DOWNLOAD_FOLDER}/interproscan-5.45-80.0-64-bit.tar.gz
+rm -f ${DOWNLOAD_FOLDER}/interproscan-5.45-80.0-64-bit.tar.gz.md5
 rm -f ${DOWNLOAD_FOLDER}/panther-data-14.1.tar.gz
 rm -f ${DOWNLOAD_FOLDER}/panther-data-14.1.tar.gz.md5

docker/scripts/unifire-workflow.sh

@@ -37,9 +37,9 @@ ${UNIFIRE_REPO}/distribution/bin/unifire.sh -r ${UNIFIRE_REPO}/samples/unirule-u
     -i ${VOLUME}/proteins_lineage-ipr.xml -t  ${UNIFIRE_REPO}/samples/unirule-templates-latest.xml \
     -o ${VOLUME}/predictions_unirule.out
 
-${UNIFIRE_REPO}/distribution/bin/unifire.sh -r ${UNIFIRE_REPO}/samples/saas-urml-latest.xml \
+${UNIFIRE_REPO}/distribution/bin/unifire.sh -r ${UNIFIRE_REPO}/samples/arba-urml-latest.xml \
     -i ${VOLUME}/proteins_lineage-ipr.xml \
-    -o ${VOLUME}/predictions_saas.out
+    -o ${VOLUME}/predictions_arba.out
 
 ${UNIFIRE_REPO}/distribution/bin/unifire.sh -n 100 -r ${UNIFIRE_REPO}/samples/unirule.pirsr-urml-latest.xml \
     -i ${VOLUME}/proteins_lineage-ipr-urml.xml -s XML -t  ${UNIFIRE_REPO}/samples/pirsr_data/PIRSR_templates.xml \
@@ -48,7 +48,7 @@ ${UNIFIRE_REPO}/distribution/bin/unifire.sh -n 100 -r ${UNIFIRE_REPO}/samples/un
 # prediction output files must belong to the same user and group as proteins.fasta input file
 ownership=`stat -c "%u:%g" ${VOLUME}/proteins.fasta`
 for outfile in  proteins_lineage.fasta proteins_lineage-ipr.xml proteins_lineage-ipr-urml.xml predictions_unirule.out \
-  predictions_saas.out predictions_unirule-pirsr.out seq aln
+  predictions_arba.out predictions_unirule-pirsr.out seq aln
 do
   chown -R ${ownership} ${VOLUME}/${outfile}
 done