add jflow and first test to get ride of ergatis

application.properties

+#
+# Copyright (C) 2012 INRA
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+[general]
+# The Typo3 pid where to link datas
+pid = 5
+# The ng6 work directory
+work_dir = /path/to/working/directory
+# The ng6 save directory
+save_dir = /path/to/saving/directory
+# The ng6 tmp directory, should be accessible 
+# from any nodes if running in a cluster 
+# environment
+tmp_dir = /path/to/tmp/directory
+
+[database]
+host = localhost
+user = typo3
+passwd = typo3
+dbname = typo3
+
+[logging]
+log_file = /home/jmariett/scratch/ng6/ng6.log
+
+[storage]
+save_directory = /home/jmariett/scratch/ngspipelines/
+working_directory = /home/jmariett/scratch/weaver
+
+[softwares]
+blastall = /usr/bin/blastall
+formatdb = /usr/bin/formatdb
+
+[454_mids]
+MID1 = ACGAGTGCGT
+MID2 = ACGCTCGACA
+MID3 = AGACGCACTC
+MID4 = AGCACTGTAG
+MID5 = ATCAGACACG
+MID6 = ATATCGCGAG
+MID7 = CGTGTCTCTA
+MID8 = CTCGCGTGTC
+MID9 = TAGTATCAGC
+MID10 = TCTCTATGCG
+MID11 = TGATACGTCT
+MID12 = TACTGAGCTA
+MID13 = CATAGTAGTG
+MID14 = CGAGAGATAC
+MID15 = ATACGACGTA
+MID16 = TCACGTACTA
+MID17 = CGTCTAGTAC
+MID18 = TCTACGTAGC
+MID19 = TGTACTACTC
+MID20 = ACGACTACAG
+MID21 = CGTAGACTAG
+MID22 = TACGAGTATG
+MID23 = TACTCTCGTG
+MID24 = TAGAGACGAG
+MID25 = TCGTCGCTCG
+MID26 = ACATACGCGT
+MID27 = ACGCGAGTAT
+MID28 = ACTACTATGT
+MID29 = ACTGTACAGT
+MID30 = AGACTATACT
+MID31 = AGCGTCGTCT
+MID32 = AGTACGCTAT
+MID33 = ATAGAGTACT
+MID34 = CACGCTACGT
+MID35 = CAGTAGACGT
+MID36 = CGACGTGACT
+MID37 = TACACACACT
+MID38 = TACACGTGAT
+MID39 = TACAGATCGT
+MID40 = TACGCTGTCT
+MID41 = TAGTGTAGAT
+MID42 = TCGATCACGT
+MID43 = TCGCACTAGT
+MID44 = TCTAGCGACT
+MID45 = TCTATACTAT
+MID46 = TGACGTATGT
+MID47 = TGTGAGTAGT
+MID48 = ACAGTATATA
+MID49 = ACGCGATCGA
+MID50 = ACTAGCAGTA
+MID51 = AGCTCACGTA
+MID52 = AGTATACATA
+MID53 = AGTCGAGAGA
+MID54 = AGTGCTACGA
+MID55 = CGATCGTATA
+MID56 = CGCAGTACGA
+MID57 = CGCGTATACA
+MID58 = CGTACAGTCA
+MID59 = CGTACTCAGA
+MID60 = CTACGCTCTA
+MID61 = CTATAGCGTA
+MID62 = TACGTCATCA
+MID63 = TAGTCGCATA
+MID64 = TATATATACA
+MID65 = TATGCTAGTA
+MID66 = TCACGCGAGA
+MID67 = TCGATAGTGA
+MID68 = TCGCTGCGTA
+MID69 = TCTGACGTCA
+MID70 = TGAGTCAGTA
+MID71 = TGTAGTGTGA
+MID72 = TGTCACACGA
+MID73 = TGTCGTCGCA
+MID74 = ACACATACGC
+MID75 = ACAGTCGTGC
+MID76 = ACATGACGAC
+MID77 = ACGACAGCTC
+MID78 = ACGTCTCATC
+MID79 = ACTCATCTAC
+MID80 = ACTCGCGCAC
+MID81 = AGAGCGTCAC
+MID82 = AGCGACTAGC
+MID83 = AGTAGTGATC
+MID84 = AGTGACACAC
+MID85 = AGTGTATGTC
+MID86 = ATAGATAGAC
+MID87 = ATATAGTCGC
+MID88 = ATCTACTGAC
+MID89 = CACGTAGATC
+MID90 = CACGTGTCGC
+MID91 = CATACTCTAC
+MID92 = CGACACTATC
+MID93 = CGAGACGCGC
+MID94 = CGTATGCGAC
+MID95 = CGTCGATCTC
+MID96 = CTACGACTGC
+MID97 = CTAGTCACTC
+MID98 = CTCTACGCTC
+MID99 = CTGTACATAC
+MID100 = TAGACTGCAC
+MID101 = TAGCGCGCGC
+MID102 = TAGCTCTATC
+MID103 = TATAGACATC
+MID104 = TATGATACGC
+MID105 = TCACTCATAC
+MID106 = TCATCGAGTC
+MID107 = TCGAGCTCTC
+MID108 = TCGCAGACAC
+MID109 = TCTGTCTCGC
+MID110 = TGAGTGACGC
+MID111 = TGATGTGTAC
+MID112 = TGCTATAGAC
+MID113 = TGCTCGCTAC
+MID114 = ACGTGCAGCG
+MID115 = ACTCACAGAG
+MID116 = AGACTCAGCG
+MID117 = AGAGAGTGTG
+MID118 = AGCTATCGCG
+MID119 = AGTCTGACTG
+MID120 = AGTGAGCTCG
+MID121 = ATAGCTCTCG
+MID122 = ATCACGTGCG
+MID123 = ATCGTAGCAG
+MID124 = ATCGTCTGTG
+MID125 = ATGTACGATG
+MID126 = ATGTGTCTAG
+MID127 = CACACGATAG
+MID128 = CACTCGCACG
+MID129 = CAGACGTCTG
+MID130 = CAGTACTGCG
+MID131 = CGACAGCGAG
+MID132 = CGATCTGTCG
+MID133 = CGCGTGCTAG
+MID134 = CGCTCGAGTG
+MID135 = CGTGATGACG
+MID136 = CTATGTACAG
+MID137 = CTCGATATAG
+MID138 = CTCGCACGCG
+MID139 = CTGCGTCACG
+MID140 = CTGTGCGTCG
+MID141 = TAGCATACTG
+MID142 = TATACATGTG
+MID143 = TATCACTCAG
+MID144 = TATCTGATAG
+MID145 = TCGTGACATG
+MID146 = TCTGATCGAG
+MID147 = TGACATCTCG
+MID148 = TGAGCTAGAG
+MID149 = TGATAGAGCG
+MID150 = TGCGTGTGCG
+MID151 = TGCTAGTCAG
+MID152 = TGTATCACAG
+MID153 = TGTGCGCGTG
+RL1 = ACACGACGACT,AGTCGTGGTGT
+RL2 = ACACGTAGTAT,ATACTAGGTGT
+RL3 = ACACTACTCGT,ACGAGTGGTGT
+RL4 = ACGACACGTAT,ATACGTGGCGT
+RL5 = ACGAGTAGACT,AGTCTACGCGT
+RL6 = ACGCGTCTAGT,ACTAGAGGCGT
+RL7 = ACGTACACACT,AGTGTGTGCGT
+RL8 = ACGTACTGTGT,ACACAGTGCGT
+RL9 = ACGTAGATCGT,ACGATCTGCGT
+RL10 = ACTACGTCTCT,AGAGACGGAGT
+RL11 = ACTATACGAGT,ACTCGTAGAGT
+RL12 = ACTCGCGTCGT,ACGACGGGAGT
+RL13 = AGACTCGACGT,ACGTCGGGTCT
+RL14 = AGTACGAGAGT,ACTCTCGGACT
+RL15 = AGTACTACTAT,ATAGTAGGACT
+RL16 = AGTAGACGTCT,AGACGTCGACT
+RL17 = AGTCGTACACT,AGTGTAGGACT
+RL18 = AGTGTAGTAGT,ACTACTAGACT
+RL19 = ATAGTATACGT,ACGTATAGTAT
+RL20 = CAGTACGTACT,AGTACGTGCTG
+RL21 = CGACGACGCGT,ACGCGTGGTCG
+RL22 = CGACGAGTACT,AGTACTGGTCG
+RL23 = CGATACTACGT,ACGTAGTGTCG
+RL24 = CGTACGTCGAT,ATCGACGGACG
+RL25 = CTACTCGTAGT,ACTACGGGTAG
+RL26 = GTACAGTACGT,ACGTACGGTAC
+RL27 = GTCGTACGTAT,ATACGTAGGAC
+RL28 = GTGTACGACGT,ACGTCGTGCAC
+RL29 = ACACAGTGAGT,ACTCACGGTGT
+RL30 = ACACTCATACT,AGTATGGGTGT
+RL31 = ACAGACAGCGT,ACGCTGTGTGT
+RL32 = ACAGACTATAT,ATATAGTGTGT
+RL33 = ACAGAGACTCT,AGAGTCTGTGT
+RL34 = ACAGCTCGTGT,ACACGAGGTGT
+RL35 = ACAGTGTCGAT,ATCGACAGTGT
+RL36 = ACGAGCGCGCT,AGCGCGCGCGT
+RL37 = ACGATGAGTGT,ACACTCAGCGT
+RL38 = ACGCGAGAGAT,ATCTCTGGCGT
+RL39 = ACGCTCTCTCT,AGAGAGGGCGT
+RL40 = ACGTCGCTGAT,ATCAGCGGCGT
+RL41 = ACGTCTAGCAT,ATGCTAGGCGT
+RL42 = ACTAGTGATAT,ATATCACGAGT
+RL43 = ACTCACACTGT,ACAGTGGGAGT
+RL44 = ACTCACTAGCT,AGCTAGGGAGT
+RL45 = ACTCTATATAT,ATATATGGAGT
+RL46 = ACTGATCTCGT,ACGAGATGAGT
+RL47 = ACTGCTGTACT,AGTACAGGAGT
+RL48 = ACTGTAGCGCT,AGCGCTAGAGT
+RL49 = AGACACTCACT,AGTGAGGGTCT
+RL50 = AGACATATAGT,ACTATAGGTCT
+RL51 = AGACGTGATCT,AGATCAGGTCT
+RL52 = AGAGTACAGAT,ATCTGTAGTCT
+RL53 = AGAGTATCTCT,AGAGATAGTCT
+RL54 = AGATACGCTGT,ACAGCGTGTCT
+RL55 = AGATCTAGTCT,AGACTAGGTCT
+RL56 = AGCAGCGTAGT,ACTACGCGGCT
+RL57 = AGCGCACGAGT,ACTCGTGGGCT
+RL58 = AGCGTGTGCGT,ACGCACAGGCT
+RL59 = AGCTAGATACT,AGTATCTGGCT
+RL60 = AGCTGTCGACT,AGTCGACGGCT
+RL61 = AGTATGCACGT,ACGTGCAGACT
+RL62 = AGTCGCGCTAT,ATAGCGGGACT
+RL63 = AGTCTGTCTGT,ACAGACGGACT
+RL64 = ATACACACGAT,ATCGTGGGTAT
+RL65 = ATACGCGTGCT,AGCACGGGTAT
+RL66 = ATACTAGCACT,AGTGCTGGTAT
+RL67 = ATAGAGCTAGT,ACTAGCTGTAT
+RL68 = ATATAGAGTAT,ATACTCTGTAT
+RL69 = ATCGCTCACGT,ACGTGAGGGAT
+RL70 = ATCGTCAGTCT,AGACTGAGGAT
+RL71 = ATCTCTCGTAT,ATACGAGGGAT
+RL72 = ATCTGAGACGT,ACGTCTCGGAT
+RL73 = ATGCTACGTCT,AGACGTGGCAT
+RL74 = ATGTGACTACT,AGTAGTCGCAT
+RL75 = CACGAGACAGT,ACTGTCTGGTG
+RL76 = CACGCGAGTCT,AGACTCGGGTG
+RL77 = CACGCTACGAT,ATCGTAGGGTG
+RL78 = CACGTGTATAT,ATATACAGGTG
+RL79 = CACTACGATGT,ACATCGTGGTG
+RL80 = CACTATACTCT,AGAGTATGGTG
+RL81 = CAGCGTACTGT,ACAGTAGGCTG
+RL82 = CAGTCTCTAGT,ACTAGAGGCTG
+RL83 = CATAGTCGCGT,ACGCGACGATG
+RL84 = CGAGACACTAT,ATAGTGTGTCG
+RL85 = CGAGAGTGTGT,ACACACTGTCG
+RL86 = CGAGTCATCGT,ACGATGAGTCG
+RL87 = CGATCGTATAT,ATATACGGTCG
+RL88 = CGCAGTACGCT,AGCGTACGGCG
+RL89 = CGCGATCGTAT,ATACGATGGCG
+RL90 = CGCGCTATACT,AGTATAGGGCG
+RL91 = CGTACAGATAT,ATATCTGGACG
+RL92 = CGTAGCTCTCT,AGAGAGCGACG
+RL93 = CGTATAGTGCT,AGCACTAGACG
+RL94 = CGTCAGCGACT,AGTCGCGGACG
+RL95 = CGTCGCAGTGT,ACACTGGGACG
+RL96 = CGTCTCACGAT,ATCGTGGGACG
+RL97 = CGTGACTCAGT,ACTGAGTGACG
+RL98 = CTACACGCTCT,AGAGCGGGTAG
+RL99 = CTACGATATGT,ACATATGGTAG
+RL100 = CTAGACAGACT,AGTCTGTGTAG
+RL101 = CTAGTACTCAT,ATGAGTAGTAG
+RL102 = CTATATGTCGT,ACGACATGTAG
+RL103 = CTATCGACACT,AGTGTCGGTAG
+RL104 = CTATGTAGAGT,ACTCTACGTAG
+RL105 = CTCACGTACAT,ATGTACGGGAG
+RL106 = CTCGAGTCTCT,AGAGACTGGAG
+RL107 = CTCGTCGAGAT,ATCTCGAGGAG
+RL108 = CTCTACAGCGT,ACGCTGTGGAG
+RL109 = CTGTCGTGCGT,ACGCACGGCAG
+RL110 = CTGTGACGTGT,ACACGTCGCAG
+RL111 = GACGCTGTCGT,ACGACAGGGTC
+RL112 = GACGTATGACT,AGTCATAGGTC
+RL113 = GACTAGCTAGT,ACTAGCTGGTC
+RL114 = GAGACGTCGCT,AGCGACGGCTC
+RL115 = GAGAGAGACGT,ACGTCTCGCTC
+RL116 = GCGTAGACTAT,ATAGTCTGCGC
+RL117 = GCGTCGTGTCT,AGACACGGCGC
+RL118 = GCTCTCTACGT,ACGTAGGGAGC
+RL119 = GTACACTGTAT,ATACAGGGTAC
+RL120 = GTACGCGACAT,ATGTCGGGTAC
+RL121 = GTACTATAGAT,ATCTATGGTAC
+RL122 = GTACTGAGTCT,AGACTCGGTAC
+RL123 = GTAGCTAGCGT,ACGCTAGGTAC
+RL124 = GTAGTCACTGT,ACAGTGAGTAC
+RL125 = GTAGTGTCACT,AGTGACAGTAC
+RL126 = GTATACATAGT,ACTATGTGTAC
+RL127 = GTCATCGTCGT,ACGACGAGGAC
+RL128 = GTCGACACGCT,AGCGTGTGGAC
+RL129 = GTCGAGTGAGT,ACTCACTGGAC
+RL130 = GTCTACTATCT,AGATAGTGGAC
+RL131 = GTGTCTAGACT,AGTCTAGGCAC
+RL132 = GTGTGTATCGT,ACGATACGCAC
\ No newline at end of file

bin/_preamble.py

+#
+# Copyright (C) 2012 INRA
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+import sys, os
+
+path = os.path.abspath(sys.argv[0])
+
+while os.path.dirname(path) != path:
+    if os.path.exists(os.path.join(path, 'jflow', '__init__.py')):
+        sys.path.insert(0, path)
+        break
+    path = os.path.dirname(path)
\ No newline at end of file

bin/ng6_cli.py

+#
+# Copyright (C) 2012 INRA
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+import sys
+import argparse
+
+try:
+    import _preamble
+except ImportError:
+    sys.exc_clear()
+
+from jflow.workflows_manager import WorkflowsManager
+from jflow.workflow import Workflow
+from ng6.project import Project
+
+
+if __name__ == '__main__':
+
+    # Create the top-level parser
+    parser = argparse.ArgumentParser(prog='ng6')
+    subparsers = parser.add_subparsers(title='Available pipelines')
+    
+    # Add project menu
+    sub_parser = subparsers.add_parser("addproject", help="Add a brand new project")
+    sub_parser.add_argument("--name", type=str, help="Give a name to your project (has to be unique)",
+                            required=True, dest="project_name", metavar="STR")
+    sub_parser.add_argument("--description", type=str, help="Give a description to your project",
+                            required=True, dest="description", metavar="STR")
+    sub_parser.add_argument("--admin-login", type=str, help="Who is the project administrator",
+                            required=True, dest="admin_login", metavar="STR")
+    sub_parser.set_defaults(cmd_object="addproject")
+    
+    # Add available pipelines
+    wf_instances = WorkflowsManager.get_workflows()
+    for instance in wf_instances:
+        # create the subparser for each applications
+        sub_parser = subparsers.add_parser(instance.name, help=instance.description)
+        for param in instance.parameters:
+            sub_parser.add_argument(param.flag, type=param.type, help=param.help,
+                                    required=param.required, dest=param.name,
+                                    metavar=param.metavar.upper(), default=param.default)
+        sub_parser.set_defaults(cmd_object=instance)
+    args = vars(parser.parse_args())
+    
+    if isinstance(args["cmd_object"], Workflow):
+        #try:
+        args["cmd_object"].execute(args)
+        #except (IOError, NameError), e: 
+        #    sys.exit("Error: " + str(e))
+    elif args["cmd_object"] == "addproject":
+        #try:
+        my_project = Project(args["project_name"], args["description"], args["admin_login"])
+        #except NameError, e:
+        #     sys.exit("Error: " + str(e))

jflow/__init__.py

+#
+# Copyright (C) 2012 INRA
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+__version__ = '1.0'
\ No newline at end of file

jflow/component.py

+#
+# Copyright (C) 2012 INRA
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+import os
+import inspect
+
+from jflow.workflows_manager import WorkflowsManager
+from jflow.config_reader import JFlowConfigReader
+from jflow.dataset import ArrayList
+
+from weaver.util import parse_string_list
+
+
+class Component(object):
+    """
+    """
+        
+    def __init__(self, is_dynamic=False):
+        """
+          @param is_dynamic: if true, this component has dynamic inputs/outputs
+        """
+        self.is_dynamic = is_dynamic
+        self.prefix = "default"
+        self.output_directory = None
+    
+    def get_outputs(self, output_list=None, input_list=None):
+        """
+        If `output_list` is a string template, then it may have the following
+        fields:
+    
+        - `{fullpath}`, `{FULL}`         -- Full input file path.
+        - `{basename}`, `{BASE}`         -- Base input file name.
+        - `{fullpath_woext}`, `{FULLWE}` -- Full input file path without extension
+        - `{basename_woext}`, `{BASEWE}` -- Base input file name without extension
+        """        
+        if output_list is None:
+            return []
+        
+        if isinstance(output_list, str):
+            if not input_list or not '{' in str(output_list):
+                return [output_list]
+            
+            return [os.path.join(self.output_directory, str(output_list).format(
+                        fullpath       = input,
+                        FULL           = input,
+                        i              = '{0:05X}'.format(i),
+                        NUMBER         = '{0:05X}'.format(i),
+                        fullpath_woext = os.path.splitext(input)[0],
+                        FULL_WOEXT     = os.path.splitext(input)[0],
+                        basename       = os.path.basename(input),
+                        BASE           = os.path.basename(input),
+                        basename_woext = os.path.splitext(os.path.basename(input))[0] if os.path.splitext(os.path.basename(input))[1] != ".gz" else os.path.splitext(os.path.splitext(os.path.basename(input))[0])[0],
+                        BASE_WOEXT     = os.path.splitext(os.path.basename(input))[0] if os.path.splitext(os.path.basename(input))[1] != ".gz" else os.path.splitext(os.path.splitext(os.path.basename(input))[0])[0]))
+                    for i, input in enumerate(parse_string_list(input_list))]
+    
+    def execute(self):
+        # first create the output directory
+        os.makedirs(self.output_directory, 0751)
+        # then run the component
+        self.run()
+    
+    def run(self):
+        """ 
+        Run the component, has to be implemented by subclasses
+        """
+        raise NotImplementedError
+    
+    def define_parameters(self, *args):
+        """ 
+        Define the component parameters, has to be implemented by subclasses
+        """
+        raise NotImplementedError
+    
+    def get_exec_path(self, software):
+        config_reader = JFlowConfigReader()
+        exec_path = config_reader.get_exec(software)
+        if exec_path is None and os.path.isfile(os.path.join(os.path.dirname(inspect.getfile(self.__class__)), software)):
+            exec_path = os.path.join(os.path.dirname(inspect.getfile(self.__class__)), software)
+        elif exec_path is None and os.path.isfile(os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "../bin", software)):
+            exec_path = os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "../bin", software)
+        elif exec_path is None and os.path.isfile(os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "bin", software)):
+            exec_path = os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "bin", software)
+        return exec_path
+    
+    def __eq__(self, other):
+        return self.__class__ == other.__class__ and self.prefix == other.prefix

jflow/components/__init__.py

+#
+# Copyright (C) 2012 INRA
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
\ No newline at end of file

jflow/components/indexing.py

+#
+# Copyright (C) 2012 INRA
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+import os
+
+from jflow.component import Component
+from jflow.utils import split_and_rename_seq, get_file_base
+
+from weaver.function import ShellFunction
+
+
+class FormatDB (Component):
+    
+    def __init__(self):
+        Component.__init__(self, is_dynamic=True)
+    
+    def define_parameters(self, input_fasta, protein=False, nb_seq_per_file=None):
+        self.input_fasta = input_fasta
+        self.protein = protein
+        self.database = os.path.join(self.output_directory, os.path.basename(input_fasta))
+    
+    def run(self):
+        # first make the symbolic link
+        os.symlink(self.input_fasta, self.database)
+        if self.protein: p = "T"
+        else: p = "F"
+        formatdb = ShellFunction(self.get_exec_path("formatdb") + " -p " + p + " -i $1 -n $2", cmd_format='{EXE} {IN} {OUT}')
+        formatdb(inputs=self.input_fasta, outputs=self.database)
+        
\ No newline at end of file

jflow/components/utils.py

+#
+# Copyright (C) 2012 INRA
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+import os
+
+from jflow.component import Component
+from jflow.utils import split_and_rename_seq, get_file_base
+
+from weaver.function import PythonFunction, ShellFunction
+from weaver.abstraction import Merge, Map
+
+
+class SplitAndRename (Component):
+    
+    def __init__(self):
+        Component.__init__(self, is_dynamic=True)
+    
+    def define_parameters(self, input_file, nb_seq_per_file=None):
+        self.input_file = input_file
+        self.nb_seq_per_file = nb_seq_per_file
+        self.renamed_seq_file = os.path.join(self.output_directory, get_file_base(input_file) + ".numeric_ids.fasta")
+        
+    def run(self):
+        rename = PythonFunction(split_and_rename_seq)
+        rename(outputs=self.renamed_seq_file, arguments=[self.input_file, self.output_directory, self.nb_seq_per_file])
+        
+class MergeFiles (Component):
+    
+    def define_parameters(self, input_files, output_file_name="merged.txt", on_basename=False):
+        self.input_files = input_files
+        self.on_basename = on_basename
+        self.merged_files = []
+        if self.on_basename:
+            self.basenames = {}
+            self.merged_basenames = {}
+            for file in self.input_files:
+                basename = os.path.basename(file).split(".")[0]
+                if self.basenames.has_key(basename):
+                    self.basenames[basename].append(file)
+                else:
+                    self.basenames[basename] = [file]
+                out_name = os.path.join(self.output_directory, basename+"_"+output_file_name)
+                if not self.merged_basenames.has_key(basename):
+                    self.merged_basenames[basename] = out_name