+++ /dev/null
-/* Copyright (c) 2011 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-package compbio.runner._impl;\r
-\r
-import java.util.Arrays;\r
-import java.util.List;\r
-\r
-import compbio.runner._SkeletalCommandBuilder;\r
-\r
-/*\r
- @see \r
- RONN does not accept stdin the file name must be defined as parameter\r
- It accepts only clear sequence, no FASTA header! \r
- It can only analyse ONE sequence per run! (or may be not, but the results gets overriden!)\r
-\r
- */\r
-public class Mcl extends _SkeletalCommandBuilder {\r
-\r
- private static final String command = "/homes/pvtroshin/soft/MclRunner.sh";\r
- // -q bigmem.q -l qname=bigmem.q,ram=8000M,h_vmem=8000M\r
- private static final String nativeSpec = " -q 64bit.q -l qname=64bit.q -l h_vmem=8000M -l ram=8000M";\r
- // Read from stdin and write to stdout\r
- private static final List<String> params = Arrays\r
- .asList(new String[] { "" }); // "-","--abc", "-o -"\r
-\r
- private final String workDirectory;\r
-\r
- public Mcl(String workDirectory) {\r
- this.workDirectory = workDirectory;\r
- }\r
-\r
- public static List<String> getTestParams() {\r
- return params;\r
- }\r
-\r
- public String getCommand(ExecProvider provider) {\r
- return command;\r
- }\r
-\r
- public static String getTestCommand() {\r
- return command;\r
- }\r
-\r
- public String getCommandName() {\r
- return "MCL";\r
- }\r
-\r
- @Override\r
- public List<String> getCreatedFiles() {\r
- // TODO Auto-generated method stub\r
- return null;\r
- }\r
-\r
- @Override\r
- public String getInput() {\r
- // TODO Auto-generated method stub\r
- return null;\r
- }\r
-\r
-}\r