Commit ec6e3180 authored by Tyler Collins's avatar Tyler Collins
Browse files

Large structure and pathing changes to move the notion of the lossless pipeline into derivatives.

parent 0edb5698
[submodule "bids/code/lossless/dependencies/eeglab_asr_amica"]
path = bids/code/lossless/dependencies/eeglab_asr_amica
url = https://git.sharcnet.ca/bucanl_eeglab_versions/eeglab_lossless.git
Subproject commit 32e79550469fbfdcf2a4c5aeed46586611d99fb7
......@@ -5,5 +5,5 @@ export OMPI_MCA_mpi_cuda_support
module purge
module load intel/17.0.1 ldwrapper torque/2.5.13 sq-tm/2.5
# Uses module-force to force loading of incompatible packages
eval `bids/code/lossless/tools/module-force load openmpi/intel/1.6.5`
eval `bids/derivatives/lossless/code/tools/module-force load openmpi/intel/1.6.5`
......@@ -3,7 +3,7 @@ log
local_project
local_dependency
bids/code/lossless/dependencies
bids/derivatives/lossless/code/dependencies
remote_user_name
user_name
remote_exec_host
......@@ -11,17 +11,17 @@ remote_exec_host
remote_project_archive
graham.computecanada.ca:/project/group_name/user_name/project_name/
remote_project_work
graham.computecanada.ca:/scratch/group_name/user_name/project_name/
graham.computecanada.ca:/scratch/user_name/project_name/
remote_dependency
graham.computecanada.ca:/scratch/group_name/user_name/project_name/bids/code/lossless/dependencies
graham.computecanada.ca:/scratch/user_name/project_name/bids/code/lossless/dependencies
mount_archive
remote_archive
mount_work
remote_work
misc
[config_dir] bids/code/lossless/config
[config_dir] bids/derivatives/lossless/code/config
[data_dir] bids/
[script_dir] bids/code/lossless/scripts
[script_dir] bids/derivatives/lossless/code/scripts
system_cmds
sshfs [remote_user_name]@[remote_project_archive] [cd]/[mount_archive]
sshfs [remote_user_name]@[remote_project_work] [cd]/[mount_work]
......
warning off;
addpath([pwd '/bids/code/lossless/dependencies/eeglab_asr_amica'], ...
[pwd '/bids/code/lossless/dependencies/matlog']);
[pwd '/bids/derivatives/lossless/code/dependencies/matlog']);
% eeglab auto loads the path correctly instead of shotgun blasting with
% addpath(genpath(<>)) as we were doing prior
......
......@@ -2,7 +2,7 @@ warning off;
pkg load signal;
addpath([pwd '/bids/code/lossless/dependencies/eeglab_asr_amica'], ...
[pwd '/bids/code/lossless/dependencies/matlog']);
[pwd '/bids/derivatives/lossless/code/dependencies/matlog']);
cd '[:,1,remote_project_work]';
% eeglab auto loads the path correctly instead of shotgun blasting with
......
......@@ -16,7 +16,7 @@ replace_string
[sd_ch_vals],[.15 .85]
[sd_ch_o],3
[sd_ch_p],.2
[ref_loc_file],bids/code/lossless/misc/standard_1020_bucanl19.elc
[ref_loc_file],bids/derivatives/lossless/code/misc/standard_1020_bucanl19.elc
[low_bound_hz],1
[high_bound_hz],30
[save_f_res],1
......@@ -34,12 +34,12 @@ replace_string
[r_t_p],.2
[min_gap_ms],2000
[out_path],bids/derivatives/lossless
[amica_param_file],bids/code/lossless/misc/amica15_default.param
[amica_param_file],bids/derivatives/lossless/code/misc/amica15_default.param
[amica_threads_s02],8
order
1
session_init
bids/code/lossless/config/octave.sesinit
bids/derivatives/lossless/code/config/octave.sesinit
job_name
[batch_hfn,.,1]_[/,-1,batch_dfn,.,-1]
mfile_name
......@@ -47,7 +47,7 @@ mfile_name
job_init
m_init
bids/code/lossless/config/octave.minit
bids/derivatives/lossless/code/config/octave.minit
submit_options
--account=def-jdesjard
memory
......
......@@ -3,19 +3,19 @@ file_name
exec_func
ef_sbatch
replace_string
[dep_path],bids/code/lossless/dependencies/eeglab_asr_amica/plugins/amica
[dep_path],bids/derivatives/lossless/code/dependencies/eeglab_asr_amica/plugins/amica
[in_path],analysis/data/2_preproc
[amica_ver],amica15
order
[2 1]
session_init
bids/code/lossless/config/amica.sesinit
bids/derivatives/lossless/code/config/amica.sesinit
job_name
[batch_hfn,.,1]_[/,-1,batch_dfn,.,-1]
mfile_name
[/,-1,batch_dfn,.,-1]
job_init
bids/code/lossless/config/amica.jobinit
bids/derivatives/lossless/code/config/amica.jobinit
m_init
submit_options
......
......@@ -12,12 +12,12 @@ replace_string
[sd_t_p],.2
[min_gap_ms],2000
[out_path],bids/derivatives/lossless
[amica_param_file],bids/code/lossless/misc/amica_default.param
[amica_param_file],bids/derivatives/lossless/code/misc/amica_default.param
[amica_threads_s07_08_09],8
order
[3 2]
session_init
bids/code/lossless/config/octave.sesinit
bids/derivatives/lossless/code/config/octave.sesinit
job_name
[batch_hfn,.,1]_[/,-1,batch_dfn,.,-1]
mfile_name
......@@ -25,7 +25,7 @@ mfile_name
job_init
m_init
bids/code/lossless/config/octave.minit
bids/derivatives/lossless/code/config/octave.minit
submit_options
--account=def-jdesjard
memory
......
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