XGrid Batch Plist File

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Back to the XGrid Pipeline page.


--Thiebaut 19:14, 21 October 2008 (UTC)

This is the contents of a PList file defining a batch job for our pipeline. The three blobs of numbers represent a coded version of the three Perl programs. Each program is actually sent to the XGrid when it is run. Similarly, if we had data files, they would get included in the PList file.

{
    jobSpecification =     {
        applicationIdentifier = DFT;
        inputFiles =         {
            "computeAminoFreq.pl" =             {
                fileData = <2321202f 7573722f 62696e2f 7065726c 202d770a 2320636f 6d707574 65416d69 6e6f4672 65712e70 6c0a2320 442e2054 68696562 6175740a 23204769 76656e20 61206669 6c652063 6f6e7461 696e696e 67205345 51524553 206c696e 6573206f 66206120 50444220 66696c65 2c20636f 6d707574 65732074 68650a23 20667265 7175656e 6379206f 66206f63 63757265 6e636520 6f662061 6c6c2074 68652061 6d696e6f 20616369 6473206c 69737465 642e0a23 20507269 6e747320 6f757420 74686520 66726571 75656e63 6965732e 0a23200a 23205379 6e746178 3a0a2320 20202020 2020202e 2f636f6d 70757465 416d696e 6f467265 712e706c 20207465 6d704669 6c650a23 0a0a232d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d0a23 20726561 6446696c 653a2072 65616473 20612066 696c6520 616e6420 72657475 726e7320 616e2061 72726179 206f6620 616c6c20 74686520 6c696e65 73206974 20636f6e 7461696e 730a232d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d0a73 75622072 65616446 696c6520 7b0a2020 20206d79 20282024 6c6f6766 696c6520 29203d20 405f3b0a 0a202020 20696620 28246c6f 6766696c 65203d7e 202f5c2e 5a2f2920 20207b20 6f70656e 28414343 4553532c 22756e63 6f6d7072 65737320 2d632024 6c6f6766 696c6520 7c22293b 207d0a20 20202065 6c736966 2028246c 6f676669 6c65203d 7e202f5c 2e677a2f 29207b20 6f70656e 28414343 4553532c 22677a69 70202d64 202d6320 246c6f67 66696c65 207c2229 3b207d0a 20202020 656c7369 66202824 6c6f6766 696c6520 3d7e202f 5c2e7a69 702f2920 7b206f70 656e2841 43434553 532c2275 6e7a6970 202d7020 246c6f67 66696c65 207c2229 3b207d0a 20202020 656c7365 207b206f 70656e28 41434345 53532c20 22246c6f 6766696c 6522293b 207d0a0a 20202020 406c696e 6573203d 203c4143 43455353 3e3b0a20 20202063 6c6f7365 28204143 43455353 20293b0a 20202020 72657475 726e2040 6c696e65 733b0a7d 0a0a0a23 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d0a 232d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 0a737562 206d6169 6e207b0a 0a202020 20246172 6763203d 20242341 52475620 2b20313b 0a0a2020 20206966 20282024 61726763 203c2031 2029207b 0a202020 20202020 20707269 6e742022 53796e74 61782063 6f6d7075 7465416d 696e6f46 7265712e 706c2066 696c656e 616d655c 6e5c6e22 3b0a2020 20202020 20206578 69742831 293b0a20 2020207d 0a202020 206d7920 2466696c 654e616d 65203d20 24415247 565b305d 3b0a2020 20206d79 20406c69 6e657320 3d207265 61644669 6c652820 2466696c 654e616d 6520293b 0a202020 206d7920 246c696e 653b0a20 2020206d 79202561 6d696e6f 73203d20 28293b0a 0a202020 20232d2d 2d207061 72736520 65616368 206c696e 65202d2d 2d0a2020 2020666f 72656163 6820246c 696e6520 2820406c 696e6573 2029207b 0a096368 6f6d7020 246c696e 653b2020 20202320 72656d6f 76652062 6c616e6b 206c696e 65732061 74207468 6520656e 640a096d 79204077 6f726473 203d2073 706c6974 28202220 222c2024 6c696e65 20293b20 20232073 706c6974 20696e74 6f20776f 7264730a 09736869 66742820 40776f72 64732029 3b202020 23207265 6d6f7665 20666972 73742034 20776f72 64730a09 73686966 74282040 776f7264 7320293b 0a097368 69667428 2040776f 72647320 293b0a09 73686966 74282040 776f7264 7320293b 0a0a0923 2d2d2d20 636f756e 7420616d 696e6f20 61636964 6573202d 2d2d0a09 6d792024 616d696e 6f3b0a09 666f7265 61636820 24616d69 6e6f2028 2040776f 72647320 29207b0a 09202020 20696620 28206578 69737473 28202461 6d696e6f 737b2024 616d696e 6f207d20 29202920 7b0a0909 24616d69 6e6f737b 2024616d 696e6f20 7d203d20 24616d69 6e6f737b 2024616d 696e6f20 7d202b20 313b0a09 20202020 7d0a0920 20202065 6c736520 7b0a0909 24616d69 6e6f737b 2024616d 696e6f20 7d203d20 313b0a09 20202020 7d0a097d 0a202020 207d0a0a 20202020 0a202020 20232d2d 2d206469 73706c61 79206669 6c656e61 6d652066 6f6c6c6f 77656420 62792061 6d696e6f 20616369 64732061 6e642023 206f6363 75727265 6e636573 202d2d2d 0a202020 20776869 6c652028 206d7920 2820246b 65792c20 2476616c 75652029 203d2065 61636828 2025616d 696e6f73 20292029 7b0a0970 72696e74 20246b65 792e2220 222e2476 616c7565 2e20225c 6e223b0a 20202020 7d0a7d0a 0a6d6169 6e28293b 0a0a0a>;
                isExecutable = YES;
            };
            "pipe.pl" =             {
                fileData = <2321202f 7573722f 62696e2f 7065726c 202d770a 23207069 70652e70 6c0a2320 442e2054 68696562 6175740a 23206361 6c6c7320 74776f20 7065726c 2070726f 6772616d 732c206f 6e652061 66746572 20746865 206f7468 65722c20 746f2066 6f726d20 61207072 6f636573 73696e67 20706970 656c696e 652e0a23 0a232053 796e7461 783a0a23 20202020 20202020 20202020 20706970 652e706c 20207064 6246696c 656e616d 65200a23 0a230a73 7562206d 61696e20 7b0a2020 20202461 72676320 3d202423 41524756 202b2031 3b0a0a20 20202023 20636865 636b2023 20617267 756d656e 7473200a 20202020 69662028 20246172 6763203c 20312029 207b0a20 20202020 20202070 72696e74 20225379 6e746178 20706970 652e706c 20706462 5f66696c 656e616d 655c6e5c 6e223b0a 20202020 20202020 65786974 2831293b 0a202020 207d0a0a 20202020 23207064 62206669 6c650a20 2020206d 79202470 64624669 6c65203d 20244152 47565b30 5d3b0a0a 20202020 23207468 65207477 6f207374 61676573 206f6620 74686520 70697065 6c696e65 2e202055 73652074 68652070 72656669 7820222e 2e2f776f 726b696e 672f2220 69662070 726f6772 616d7320 61726520 746f2072 756e206f 6e205847 72696420 0a202020 20236d79 20247072 6f673120 3d20222e 2f737472 6970416d 696e6f2e 706c2024 70646246 696c6520 64656c65 74656d65 223b0a20 20202023 6d792024 70726f67 32203d20 222e2f63 6f6d7075 7465416d 696e6f46 7265712e 706c2064 656c6574 656d6522 3b0a0a20 2020206d 79202470 726f6731 203d2022 2e2e2f77 6f726b69 6e672f73 74726970 416d696e 6f2e706c 20247064 6246696c 65206465 6c657465 6d65223b 0a202020 206d7920 2470726f 6732203d 20222e2e 2f776f72 6b696e67 2f636f6d 70757465 416d696e 6f467265 712e706c 2064656c 6574656d 65223b0a 20202020 0a202020 20232073 74617274 20656163 68207072 6f677261 6d2c206f 6e652061 66746572 20746865 206f7468 6572200a 20202020 6d792024 72657456 616c7565 203d2073 79737465 6d282024 70726f67 3120293b 0a0a2020 20206966 20282024 72657456 616c7565 3d3d3020 29207b0a 20202020 20202020 20247265 7456616c 7565203d 20247265 7456616c 7565206f 72207379 7374656d 28202470 726f6732 20293b0a 20202020 7d0a2020 20202320 72657475 726e2063 6f6d6269 6e652072 65747572 6e207661 6c756573 0a202020 20726574 75726e20 24726574 56616c75 653b0a7d 0a0a6d61 696e2829 3b0a>;
                isExecutable = YES;
            };
            "stripAmino.pl" =             {
                fileData = <2321202f 7573722f 62696e2f 7065726c 202d770a 23206765 74537461 74732e70 6c0a2320 442e2054 68696562 6175740a 23204120 73696d70 6c652070 65726c20 70726f67 72616d20 74686174 20646973 706c6179 73207468 65206e75 6d626572 206f6620 6f636375 7272656e 63657320 0a23206f 6620616d 696e6f20 61636964 7320696e 20612070 726f7465 696e2773 20706462 2066696c 652e0a23 0a232053 796e7461 783a0a23 20202020 20202020 2063686d 6f64202b 78206765 74537461 74732e70 6c0a2320 20202020 20202020 2e2f6765 74537461 74732e70 6c202031 61356233 2e706462 2e677a0a 230a7573 6520204c 57503a3a 53696d70 6c653b0a 6d792024 55524c20 3d202268 7474703a 2f2f7867 7269646d 61632e64 796e646e 732e6f72 672f7e74 68696562 6175742f 70646246 696c6573 2f223b0a 0a232d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d0a232d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d0a73 75622072 65616457 65624669 6c65207b 0a202020 206d7920 2820246c 6f676669 6c652029 203d2040 5f3b0a0a 20202020 6d792024 75726c20 3d202455 524c202e 20246c6f 6766696c 653b0a20 20202075 6e6c6573 73202820 64656669 6e656428 2024636f 6e74656e 743d6765 74282024 75726c20 29202929 207b0a09 64696520 22436f75 6c64206e 6f742067 65742024 75726c5c 6e223b0a 20202020 7d0a2020 2020406c 696e6573 203d2073 706c6974 2820275c 6e272c20 24636f6e 74656e74 20293b0a 20202020 72657475 726e2040 6c696e65 733b0a7d 0a0a232d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d0a23 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d2d 2d2d2d0a 73756220 6d61696e 207b0a20 20202024 61726763 203d2024 23415247 56202b20 313b0a0a 20202020 69662028 20246172 6763203c 20312029 207b0a09 7072696e 74202253 796e7461 78207374 72697041 6d696e6f 2e706c20 66696c65 6e616d65 5c6e5c6e 223b0a09 65786974 2831293b 0a202020 207d0a20 2020206d 79202474 656d7046 696c6520 3d202264 656c6574 656d652e 31223b0a 20202020 69662028 20246172 6763203e 3d203220 29207b0a 09247465 6d704669 6c65203d 20202441 5247565b 315d3b0a 20202020 7d0a0a20 20202023 2d2d2d20 67657420 74686520 6c696e65 73206f66 20746865 2066696c 65202d2d 2d0a2020 20206d79 20406c69 6e657320 3d207265 61645765 6246696c 65282024 41524756 5b305d20 293b0a0a 20202020 6d792024 6c696e65 3b0a2020 20206d79 2025616d 696e6f73 203d2028 293b0a0a 20202020 232d2d2d 20706172 73652065 61636820 6c696e65 202d2d2d 0a202020 206f7065 6e282054 454d502c 20223e3e 20247465 6d704669 6c652220 293b0a20 20202066 6f726561 63682024 6c696e65 20282040 6c696e65 73202920 7b0a0969 66202820 246c696e 65203d7e 202f5e53 45515245 532f2029 207b0a09 20202020 63686f6d 7020246c 696e653b 20202020 23207265 6d6f7665 20626c61 6e6b206c 696e6573 20617420 74686520 656e640a 09202020 20707269 6e742054 454d5020 246c696e 65202e20 225c6e22 3b0a0920 20202070 72696e74 20246c69 6e65202e 20225c6e 223b0a09 7d0a2020 20207d0a 20202020 636c6f73 65282054 454d5020 293b0a7d 0a0a6d61 696e2829 3b0a>;
                isExecutable = YES;
            };
        };
        name = AminoPipe3;
        schedulerHints =         {
            0 = mathgrid4;
        };
        submissionIdentifier = "A simple pipe processing a PDB file";
        taskSpecifications =         {
            0 =             {
                arguments =                 (
                    "pdb100d.ent",
                    "../working/deleteme"
                );
                command = "../working/pipe.pl";
            };
        };
    };
}