From 8249fb5b6000fab0fe195ba000a175b4354fdd07 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Tue, 7 Aug 2018 14:11:31 +0100
Subject: [PATCH] Upgrade IPS to use a container

Co-authored-by: Ola Tarkowska <olat@ebi.ac.uk>
Co-authored-by: Maxim Scheremetjew <maxim@ebi.ac.uk>
---
 ...can5.21-60.cwl => InterProScan5.30-69.cwl} | 48 ++++++++++++++-----
 workflows/functional_analysis.cwl             |  2 +-
 2 files changed, 37 insertions(+), 13 deletions(-)
 rename tools/{InterProScan5.21-60.cwl => InterProScan5.30-69.cwl} (67%)

diff --git a/tools/InterProScan5.21-60.cwl b/tools/InterProScan5.30-69.cwl
similarity index 67%
rename from tools/InterProScan5.21-60.cwl
rename to tools/InterProScan5.30-69.cwl
index dbb72e4..0658599 100644
--- a/tools/InterProScan5.21-60.cwl
+++ b/tools/InterProScan5.30-69.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 
@@ -11,20 +12,22 @@ doc: |
       https://github.com/ebi-pf-team/interproscan/wiki/HowToRun
 
 requirements:
-  ResourceRequirement:
-    ramMin: 10240
-    coresMin: 3
   SchemaDefRequirement:
     types: 
       - $import: InterProScan-apps.yaml
       - $import: InterProScan-protein_formats.yaml
+  DockerRequirement:
+    dockerPull: 'biocontainers/interproscan:v5.30-69.0_cv1'
+  ShellCommandRequirement: {}
 hints:
   SoftwareRequirement:
     packages:
       interproscan:
         specs: [ "https://identifiers.org/rrid/RRID:SCR_005829" ]
-        version: [ "5.21-60" ]
-
+        version: [ "5.30-69" ]
+  ResourceRequirement:
+    ramMin: 8192
+    coresMin: 3
 inputs:
   proteinFile:
     type: File
@@ -39,19 +42,40 @@ inputs:
     inputBinding:
       itemSeparator: ','
       prefix: --applications
+  databases: Directory
 
-baseCommand: interproscan.sh
+baseCommand: []  # interproscan.sh
 
 arguments:
- - valueFrom: $(inputs.proteinFile.nameroot).i5_annotations
-   prefix: --outfile
- - valueFrom: TSV
-   prefix: --formats
+ - cp
+ - -r
+ - /opt/interproscan
+ - $(runtime.outdir)/interproscan
+ - ;
+
+ - rm
+ - -rf
+ - $(runtime.outdir)/interproscan/data
+ - ;
+
+ - cp
+ - -rs
+ - $(inputs.databases.path)/data
+ - $(runtime.outdir)/interproscan/
+ - ;
+
+ - bash
+ - $(runtime.outdir)/interproscan/interproscan.sh
+
+ - prefix: --outfile
+   valueFrom: $(runtime.outdir)/$(inputs.proteinFile.nameroot).i5_annotations
+ - prefix: --formats
+   valueFrom: TSV
  - --disable-precalc
  - --goterms
  - --pathways
- - valueFrom: $(runtime.tmpdir)
-   prefix: --tempdir
+ - prefix: --tempdir
+   valueFrom: $(runtime.tmpdir)
 
 
 outputs:
diff --git a/workflows/functional_analysis.cwl b/workflows/functional_analysis.cwl
index 911f8d8..a5589a1 100644
--- a/workflows/functional_analysis.cwl
+++ b/workflows/functional_analysis.cwl
@@ -45,7 +45,7 @@ steps:
     doc: |
       Matches are generated against predicted CDS, using a sub set of databases
       (Pfam, TIGRFAM, PRINTS, PROSITE patterns, Gene3d) from InterPro. 
-    run: ../tools/InterProScan5.21-60.cwl
+    run: ../tools/InterProScan5.30-69.cwl
     in:
       proteinFile: chunk_inputs/chunks
       applications: