Updated linux test scripts.

scripts/linux/0_linux_intro.sh

@@ -29,6 +29,7 @@ tar -xzvf files.tar.gz
 echo "6 Copying and moving files"
 mv important_results/temp_file-1 backed_up_proj_folder/
 mv important_results/dna_data_analysis_result_file_that_is_important-you_should_really_use_tab_completion_for_file_names.bam backed_up_proj_folder/
+rm -rf a_better_name
 mv a_strange_name a_better_name
 ls -l
 cp backed_up_proj_folder/last_years_data external_hdd/

scripts/linux/3_linux_pipelines.sh

@@ -8,7 +8,7 @@ projid=${1:?No projid specified (required).}
 user=${2:-$USER}
 
 # copy files for lab
-mkdir /proj/$projid/nobackup/$user/uppmax_pipeline_exercise
+mkdir -p /proj/$projid/nobackup/$user/uppmax_pipeline_exercise
 cp -r /sw/courses/ngsintro/linux/uppmax_pipeline_exercise/data/* /proj/$projid/nobackup/$user/uppmax_pipeline_exercise
 cd /proj/$projid/nobackup/$user/uppmax_pipeline_exercise
 
@@ -19,9 +19,9 @@ export PATH=$PATH:/sw/courses/ngsintro/linux/uppmax_pipeline_exercise/dummy_scri
 filter_reads -h
 
 cd /proj/$projid/nobackup/$user/uppmax_pipeline_exercise/exomeSeq
-filter_reads -i raw_data/my_reads.rawdata.fastq -o raw_data/my_reads.filtered.fastq
-align_reads -i raw_data/my_reads.filtered.fastq -o my_reads.filtered.sam -r /sw/data/uppnex/reference/Homo_sapiens/hg19/concat_rm/Homo_sapiens.GRCh37.57.dna_rm.concat.fa
-find_snps -i raw_data/my_reads.filtered.fastq -o my_reads.filtered.vcf -r /sw/data/uppnex/reference/Homo_sapiens/hg19/concat_rm/Homo_sapiens.GRCh37.57.dna_rm.concat.fa
+filter_reads -d -i raw_data/my_reads.rawdata.fastq -o raw_data/my_reads.filtered.fastq
+align_reads -d -i raw_data/my_reads.filtered.fastq -o my_reads.filtered.sam -r /sw/data/uppnex/reference/Homo_sapiens/hg19/concat_rm/Homo_sapiens.GRCh37.57.dna_rm.concat.fa
+find_snps -d -i raw_data/my_reads.filtered.fastq -o my_reads.filtered.vcf -r /sw/data/uppnex/reference/Homo_sapiens/hg19/concat_rm/Homo_sapiens.GRCh37.57.dna_rm.concat.fa
 
 
 

scripts/linux/4_linux_filetypes.sh

@@ -16,11 +16,11 @@ tree
 export PATH=$PATH:/sw/courses/ngsintro/linux/uppmax_pipeline_exercise/dummy_scripts
 
 # run programs
-reference_indexer -r 0_ref/ad2.fa
-align_reads -r 0_ref/ad2.fa -i 0_seq/ad2.fq -o 1_alignment/ad2.sam
-sambam_tool -f bam -i 1_alignment/ad2.sam -o 2_bam/ad2.bam
-sambam_tool -f sort -i 2_bam/ad2.bam -o 3_sorted/ad2.sorted.bam
-sambam_tool -f index -i 3_sorted/ad2.sorted.bam
+reference_indexer -d -r 0_ref/ad2.fa
+align_reads -d -r 0_ref/ad2.fa -i 0_seq/ad2.fq -o 1_alignment/ad2.sam
+sambam_tool -d -f bam -i 1_alignment/ad2.sam -o 2_bam/ad2.bam
+sambam_tool -d -f sort -i 2_bam/ad2.bam -o 3_sorted/ad2.sorted.bam
+sambam_tool -d -f index -i 3_sorted/ad2.sorted.bam
 mv 3_sorted/ad2.sorted.bam.bai 3_sorted/ad2.sorted.bai
 
 # cram

scripts/linux/test_all.sh

@@ -0,0 +1,37 @@
+#!/bin/bash -l
+
+set -x # print commands before executing
+set -e # exit on errors
+
+# get projid or die trying
+projid=${1:?No projid specified (required).}
+
+echo "Starting script 0"
+bash 0_linux_intro.sh $projid
+echo "Ended script 0"
+
+echo "Starting script 1"
+bash 1_linux_advanced.sh $projid
+echo "Ended script 1"
+
+echo "Starting script 2"
+bash 2_linux_uppmax.sh $projid
+echo "Ended script 2"
+
+echo "Starting script 3"
+bash 3_linux_pipelines.sh $projid
+echo "Ended script 3"
+
+echo "Starting script 4"
+bash 4_linux_filetypes.sh $projid
+echo "Ended script 4"
+
+echo """
+  ____  _   _  ____ ____ _____ ____ ____  
+ / ___|| | | |/ ___/ ___| ____/ ___/ ___| 
+ \___ \| | | | |  | |   |  _| \___ \___ \ 
+  ___) | |_| | |__| |___| |___ ___) |__) |
+ |____/ \___/ \____\____|_____|____/____/ 
+                                          
+All test ran without errors.
+"""