Merge pull request #4 from bmatern/master

EMBL-Submission initial release

HEADER

@@ -0,0 +1,16 @@
+# This file is part of EMBL-HLA-Submission.
+#
+# EMBL-HLA-Submission is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# EMBL-HLA-Submission 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 Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with EMBL-HLA-Submission. If not, see <http://www.gnu.org/licenses/>.
+
+# Version 1.0

MakeExecutables.bat

@@ -0,0 +1,34 @@
+:: This file is part of EMBL-HLA-Submission.
+::
+:: EMBL-HLA-Submission is free software: you can redistribute it and/or modify
+:: it under the terms of the GNU Lesser General Public License as published by
+:: the Free Software Foundation, either version 3 of the License, or
+:: (at your option) any later version.
+::
+:: EMBL-HLA-Submission 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 Lesser General Public License for more details.
+::
+:: You should have received a copy of the GNU Lesser General Public License
+:: along with EMBL-HLA-Submission. If not, see <http://www.gnu.org/licenses/>.
+
+:: Version 1.0
+
+:: This bat file is intended to create an executable for the windows environment.  
+:: It uses Anaconda for python 2.7 to keep track of packages. 
+
+:: See the file README.MD for how to set up your anaconda environment.
+
+:: Please verify that your files are set up such that the files exist here::
+:: C:\MinIONScripts\AlleleSubmission\MakeExecutables.bat
+:: If that is a problem, Modify the spec file "AlleleSubInstallerOptions_Windows.spec" as your needs require.
+
+SET CodePath=C:\MUMCScripts\EMBL-HLA-Submission\src
+SET BinPath=C:\MUMCScripts\EMBL-HLA-Submission\bin
+SET SpecFile=AlleleSubInstallerOptions_Windows.spec
+SET CondaEnvironment=AlleleSubEnvironment
+
+:: Run Pyinstaller to create executables
+cd %CodePath%
+activate %CondaEnvironment% && pyinstaller %SpecFile% --distpath %BinPath% && deactivate

MakeExecutables.sh

@@ -0,0 +1,29 @@
+# This file is part of EMBL-HLA-Submission.
+#
+# EMBL-HLA-Submission is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# EMBL-HLA-Submission 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 Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with EMBL-HLA-Submission. If not, see <http://www.gnu.org/licenses/>.
+
+# Version 1.0
+
+# This isn't working in it's current state.  The spec file is apparently just for windows, 
+# it's still pulling in windows DLLs.  
+# Maybe *you* want to make this file work, I just don't think it's necessary.
+
+# If you're a linux user, you should run the program using Run_allele_submission.sh.
+
+# TODO: Make a linux specific pyinstaller spec file that works.
+
+
+#source activate AlleleSubEnvironment
+#python /home/ben/Pyinstaller/PyInstaller-3.2/pyinstaller.py AlleleSubInstallerOptions.spec
+#source deactivate

Run_allele_submission.bat

@@ -0,0 +1,21 @@
+:: This file is part of EMBL-HLA-Submission.
+::
+:: EMBL-HLA-Submission is free software: you can redistribute it and/or modify
+:: it under the terms of the GNU Lesser General Public License as published by
+:: the Free Software Foundation, either version 3 of the License, or
+:: (at your option) any later version.
+::
+:: EMBL-HLA-Submission 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 Lesser General Public License for more details.
+::
+:: You should have received a copy of the GNU Lesser General Public License
+:: along with EMBL-HLA-Submission. If not, see <http://www.gnu.org/licenses/>.
+
+:: Version 1.0
+
+:: See the file README.MD for how to set up your anaconda environment.
+
+activate AlleleSubEnvironment && python AlleleSubmissionEMBL.py && deactivate
+

Run_allele_submission.sh

@@ -0,0 +1,26 @@
+# This file is part of EMBL-HLA-Submission.
+#
+# EMBL-HLA-Submission is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# EMBL-HLA-Submission 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 Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with EMBL-HLA-Submission. If not, see <http://www.gnu.org/licenses/>.
+
+# Version 1.0
+
+# See the file README.MD for how to set up your anaconda environment.
+
+cd src
+
+source activate AlleleSubEnvironment
+python AlleleSubmissionEMBL.py
+source deactivate
+
+