Commit aaf736be authored by Leon-Charles Tranchevent's avatar Leon-Charles Tranchevent
Browse files

Refactoring step 07 to process all datasets at once (Part I).

parent 69511fa6
#!/bin/bash -l
#SBATCH -J geneder:17:cp_enrich
#SBATCH -J geneder:07:cp_enrich
#SBATCH --mail-type=all
#SBATCH --mail-user=leon-charles.tranchevent@uni.lu
#SBATCH -N 1
#SBATCH -n 25
#SBATCH --time=0-06:00:00
#SBATCH --time=0-08:00:00
#SBATCH -p batch
#SBATCH --qos=qos-batch
#SBATCH --qos=normal
echo "== Starting run at $(date)"
echo "== Job ID: ${SLURM_JOBID}"
......@@ -15,9 +15,9 @@ echo "== Submit dir. : ${SLURM_SUBMIT_DIR}"
echo ""
# Defining global parameters.
INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/16/
OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/17/
CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/17-Enrichment_all/
INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/06/
OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/07/
CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/07-Enrichment/
# Loading modules.
module load lang/R/3.6.0-foss-2019a-bare
......
#!/bin/bash -l
#SBATCH -J geneder:17:g2p_enrich
#SBATCH -J geneder:07:g2p_enrich
#SBATCH --mail-type=all
#SBATCH --mail-user=leon-charles.tranchevent@uni.lu
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --time=0-15:00:00
#SBATCH --time=0-19:00:00
#SBATCH -p batch
#SBATCH --qos=qos-batch
#SBATCH --qos=normal
echo "== Starting run at $(date)"
echo "== Job ID: ${SLURM_JOBID}"
......@@ -15,9 +15,9 @@ echo "== Submit dir. : ${SLURM_SUBMIT_DIR}"
echo ""
# Defining global parameters.
INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/16/
OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/17/
CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/17-Enrichment_all/
INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/06/
OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/07/
CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/07-Enrichment/
# Loading modules.
module load lang/R/3.6.0-foss-2019a-bare
......
INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/16/
OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/17/
CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/17-Enrichment_all/
INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/06/
OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/07/
CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/07-Enrichment/
clean:
@rm -rf *~
......@@ -13,9 +13,9 @@ enrich:
@sbatch ${CODE_FOLDER}CP_enrich.sh
@sbatch ${CODE_FOLDER}G2P_enrich.sh
@sbatch ${CODE_FOLDER}ROT_enrich.sh
pfenrich:
@/bin/bash ${CODE_FOLDER}PF_enrich.sh
#merge:
# @sbatch ${CODE_FOLDER}merge.sh
##pfenrich:
## @/bin/bash ${CODE_FOLDER}PF_enrich.sh
##merge:
## @sbatch ${CODE_FOLDER}merge.sh
gsp:
@sbatch ${CODE_FOLDER}gender_specific_pathways.sh
#!/bin/bash -l
# Defining global parameters.
INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/16/
OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/17/
CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/17-Enrichment_all/
INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/06/
OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/07/
CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/07-Enrichment/
# Actual jobs
#xvfb-run Rscript --vanilla ${CODE_FOLDER}/PF_enrich.R > ${OUTPUT_FOLDER}/PF_enrich_log.out 2> ${OUTPUT_FOLDER}/PF_enrich_log.err
......
......@@ -26,7 +26,7 @@ make gsp
```
# Prerequisites
A prerequisite is to have the results of the second integration (MA+RS, step 16).
A prerequisite is to have the results of the integration (step 06).
#TODO
This steps needs to be completely changed as to incorporate the latest change in the workflow (new rankings and so on).
#!/bin/bash -l
#SBATCH -J geneder:17:rot_enrich
#SBATCH -J geneder:07:rot_enrich
#SBATCH --mail-type=all
#SBATCH --mail-user=leon-charles.tranchevent@uni.lu
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --time=0-18:00:00
#SBATCH --time=0-22:00:00
#SBATCH -p batch
#SBATCH --qos=qos-batch
#SBATCH --qos=normal
echo "== Starting run at $(date)"
echo "== Job ID: ${SLURM_JOBID}"
......@@ -15,9 +15,9 @@ echo "== Submit dir. : ${SLURM_SUBMIT_DIR}"
echo ""
# Defining global parameters.
INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/16/
OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/17/
CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/17-Enrichment_all/
INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/06/
OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/07/
CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/07-Enrichment/
# Loading modules.
module load lang/R/3.6.0-foss-2019a-bare
......
#!/bin/bash -l
#SBATCH -J geneder:17:gsp
#SBATCH -J geneder:07:gsp
#SBATCH --mail-type=all
#SBATCH --mail-user=leon-charles.tranchevent@uni.lu
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --time=0-00:01:00
#SBATCH -p batch
#SBATCH --qos=qos-batch
#SBATCH --qos=normal
echo "== Starting run at $(date)"
echo "== Job ID: ${SLURM_JOBID}"
......@@ -15,9 +15,9 @@ echo "== Submit dir. : ${SLURM_SUBMIT_DIR}"
echo ""
# Defining global parameters.
INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/16/
OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/17/
CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/17-Enrichment_all/
INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/06/
OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/07/
CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/07-Enrichment/
# Loading modules.
module load lang/R/3.6.0-foss-2019a-bare
......
local_input_data_dir: !!str '06/'
local_data_dir: !!str '07/'
local_code_dir: !!str '07-Enrichment/'
#!/bin/bash -l
#SBATCH -J geneder:17:merge
#SBATCH -J geneder:07:merge
#SBATCH --mail-type=all
#SBATCH --mail-user=leon-charles.tranchevent@uni.lu
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --time=0-00:01:00
#SBATCH -p batch
#SBATCH --qos=qos-batch
#SBATCH --qos=normal
echo "== Starting run at $(date)"
echo "== Job ID: ${SLURM_JOBID}"
......@@ -15,9 +15,9 @@ echo "== Submit dir. : ${SLURM_SUBMIT_DIR}"
echo ""
# Defining global parameters.
INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/16/
OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/17/
CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/17-Enrichment_all/
INPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/06/
OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/07/
CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/07-Enrichment/
# Loading modules.
module load lang/R/3.6.0-foss-2019a-bare
......
local_input_data_dir: !!str '16/'
local_data_dir: !!str '17/'
local_code_dir: !!str '17-Enrichment_all/'
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment