diff --git a/content/applications/app_specific/allinea_profiling_and_debugging/allinea_performance_reports/blast_with_allinea_performance_reports.md b/content/applications/app_specific/allinea_profiling_and_debugging/allinea_performance_reports/blast_with_allinea_performance_reports.md
index ec4291ed4d4fb318fac1d71327279306107d2bb2..d0a891d8fd37be998fc92e316c33fd957e46b7fa 100644
--- a/content/applications/app_specific/allinea_profiling_and_debugging/allinea_performance_reports/blast_with_allinea_performance_reports.md
+++ b/content/applications/app_specific/allinea_profiling_and_debugging/allinea_performance_reports/blast_with_allinea_performance_reports.md
@@ -9,7 +9,7 @@ with Allinea Performance Reports (`perf-report`) on Crane is shown below:
 
 {{% panel theme="info" header="blastn_perf_report.submit" %}}
 {{< highlight batch >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=BlastN
 #SBATCH --nodes=1
 #SBATCH --ntasks=16
diff --git a/content/applications/app_specific/allinea_profiling_and_debugging/allinea_performance_reports/lammps_with_allinea_performance_reports.md b/content/applications/app_specific/allinea_profiling_and_debugging/allinea_performance_reports/lammps_with_allinea_performance_reports.md
index cdb774983281fba161e0244c1496bd0b8dfd49e6..eae0db2a90c70697ea3a16bc610b05ebf62ad412 100644
--- a/content/applications/app_specific/allinea_profiling_and_debugging/allinea_performance_reports/lammps_with_allinea_performance_reports.md
+++ b/content/applications/app_specific/allinea_profiling_and_debugging/allinea_performance_reports/lammps_with_allinea_performance_reports.md
@@ -9,7 +9,7 @@ below:
 
 {{% panel theme="info" header="lammps_perf_report.submit" %}}
 {{< highlight batch >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=LAMMPS
 #SBATCH --ntasks=64
 #SBATCH --time=12:00:00
diff --git a/content/applications/app_specific/allinea_profiling_and_debugging/allinea_performance_reports/ray_with_allinea_performance_reports.md b/content/applications/app_specific/allinea_profiling_and_debugging/allinea_performance_reports/ray_with_allinea_performance_reports.md
index 28b25aa5027206c22b448fe4544288dd6ee91630..1a21e017817b79a4d2a478c6774169b7a08a8a86 100644
--- a/content/applications/app_specific/allinea_profiling_and_debugging/allinea_performance_reports/ray_with_allinea_performance_reports.md
+++ b/content/applications/app_specific/allinea_profiling_and_debugging/allinea_performance_reports/ray_with_allinea_performance_reports.md
@@ -8,7 +8,7 @@ with Allinea PerformanceReports (`perf-report`) is shown below:
 
 {{% panel theme="info" header="ray_perf_report.submit" %}}
 {{< highlight batch >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Ray
 #SBATCH --ntasks-per-node=16
 #SBATCH --time=10:00:00
diff --git a/content/applications/app_specific/bioinformatics_tools/alignment_tools/blast/create_local_blast_database.md b/content/applications/app_specific/bioinformatics_tools/alignment_tools/blast/create_local_blast_database.md
index 4caf0d48eced0f41236b698dbb744b15f4b29709..d01dfee4efef219f8eef827a38c7d688773748d7 100644
--- a/content/applications/app_specific/bioinformatics_tools/alignment_tools/blast/create_local_blast_database.md
+++ b/content/applications/app_specific/bioinformatics_tools/alignment_tools/blast/create_local_blast_database.md
@@ -15,7 +15,7 @@ where **input_reads.fasta** is the input file containing all sequences that need
 Simple example of how **makeblastdb** can be run on Crane using SLURM script and nucleotide database is shown below:
 {{% panel header="`blast_db.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Blast_DB
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=1
diff --git a/content/applications/app_specific/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md b/content/applications/app_specific/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md
index 9f8f603efd81ad53bfba8b46a01480dbc91cdb49..4c2ffc08a933dddfb5861fd53fe942bb50220221 100644
--- a/content/applications/app_specific/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md
+++ b/content/applications/app_specific/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md
@@ -52,7 +52,7 @@ Basic SLURM example of nucleotide BLAST run against the non-redundant **nt** BL
 
 {{% panel header="`blastn_alignment.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=BlastN
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
@@ -92,7 +92,7 @@ Basic SLURM example of protein BLAST run against the non-redundant **nr **BLAS
 
 {{% panel header="`blastx_alignment.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=BlastX
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
diff --git a/content/applications/app_specific/bioinformatics_tools/alignment_tools/blat.md b/content/applications/app_specific/bioinformatics_tools/alignment_tools/blat.md
index 9113bca24e2af8b1d905f63d87835b1ff65d4ac5..6d41e9c93483121dd0b213a4bfce3c77d47e3ab9 100644
--- a/content/applications/app_specific/bioinformatics_tools/alignment_tools/blat.md
+++ b/content/applications/app_specific/bioinformatics_tools/alignment_tools/blat.md
@@ -24,7 +24,7 @@ $ blat
 Running BLAT on Crane with query file `input_reads.fasta` and database `db.fa` is shown below:
 {{% panel header="`blat_alignment.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Blat
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=1
diff --git a/content/applications/app_specific/bioinformatics_tools/alignment_tools/bowtie.md b/content/applications/app_specific/bioinformatics_tools/alignment_tools/bowtie.md
index 41aaf03dbb2c4177d1e9e0fbbf471b88fe9345e2..ae79a451468afd15f08c0c926c5b8dcf76e07d3c 100644
--- a/content/applications/app_specific/bioinformatics_tools/alignment_tools/bowtie.md
+++ b/content/applications/app_specific/bioinformatics_tools/alignment_tools/bowtie.md
@@ -28,7 +28,7 @@ Bowtie supports both single-end (`input_reads.[fasta|fastq]`) and paired-end (`
 An example of how to run Bowtie alignment on Crane with single-end fastq file and `8 CPUs` is shown below:
 {{% panel header="`bowtie_alignment.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Bowtie
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
diff --git a/content/applications/app_specific/bioinformatics_tools/alignment_tools/bowtie2.md b/content/applications/app_specific/bioinformatics_tools/alignment_tools/bowtie2.md
index 8d091433c32099f6cd7e05525f9f4b722adb7bae..f6054dbf87a9768c348adc99f64c9e507c77b1c2 100644
--- a/content/applications/app_specific/bioinformatics_tools/alignment_tools/bowtie2.md
+++ b/content/applications/app_specific/bioinformatics_tools/alignment_tools/bowtie2.md
@@ -34,7 +34,7 @@ where **index_prefix** is the generated index using the **bowtie2-build** co
 An example of how to run Bowtie2 local alignment on Crane with paired-end fasta files and `8 CPUs` is shown below:
 {{% panel header="`bowtie2_alignment.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Bowtie2
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
diff --git a/content/applications/app_specific/bioinformatics_tools/alignment_tools/bwa/running_bwa_commands.md b/content/applications/app_specific/bioinformatics_tools/alignment_tools/bwa/running_bwa_commands.md
index 02ad668349887eea242ae8f31fe3c84a1cf803b6..7e96edbcf770fe804cbd6d8e6606c043dbba705d 100644
--- a/content/applications/app_specific/bioinformatics_tools/alignment_tools/bwa/running_bwa_commands.md
+++ b/content/applications/app_specific/bioinformatics_tools/alignment_tools/bwa/running_bwa_commands.md
@@ -25,7 +25,7 @@ where **index_prefix** is the index for the reference genome generated from **bw
 Simple SLURM script for running **bwa mem** on Crane with paired-end fastq input data, `index_prefix` as reference genome index, SAM output file and `8 CPUs` is shown below:
 {{% panel header="`bwa_mem.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Bwa_Mem
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
diff --git a/content/applications/app_specific/bioinformatics_tools/alignment_tools/clustal_omega.md b/content/applications/app_specific/bioinformatics_tools/alignment_tools/clustal_omega.md
index 6aeebfae3f8913f7cb4f333b94701bad3eca6a41..95b625b2ec7f5198d57434ce2ae2472e9fc16e68 100644
--- a/content/applications/app_specific/bioinformatics_tools/alignment_tools/clustal_omega.md
+++ b/content/applications/app_specific/bioinformatics_tools/alignment_tools/clustal_omega.md
@@ -33,7 +33,7 @@ $ clustalo -h
 Running Clustal Omega on Crane with input file `input_reads.fasta` with `8 threads` and `10GB memory` is shown below:
 {{% panel header="`clustal_omega.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Clustal_Omega
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
diff --git a/content/applications/app_specific/bioinformatics_tools/alignment_tools/tophat_tophat2.md b/content/applications/app_specific/bioinformatics_tools/alignment_tools/tophat_tophat2.md
index b80475689224d4b58f329dd4215c66f04b5d8f39..c0590f6a8a2d5994e10249e0c100afb762f58e0e 100644
--- a/content/applications/app_specific/bioinformatics_tools/alignment_tools/tophat_tophat2.md
+++ b/content/applications/app_specific/bioinformatics_tools/alignment_tools/tophat_tophat2.md
@@ -30,7 +30,7 @@ Prior running TopHat/TopHat2, an index from the reference genome should be built
 An example of how to run TopHat2 on Crane with paired-end fastq files `input_reads_pair_1.fastq` and `input_reads_pair_2.fastq`, reference index `index_prefix` and `8 CPUs` is shown below:
 {{% panel header="`tophat2_alignment.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Tophat2
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
diff --git a/content/applications/app_specific/bioinformatics_tools/biodata_module.md b/content/applications/app_specific/bioinformatics_tools/biodata_module.md
index c4b7c0a3037fc24efbac7e684fff85f6fd40c061..9775036525e50b6dd0a0a25a2e64b288dc20c8e0 100644
--- a/content/applications/app_specific/bioinformatics_tools/biodata_module.md
+++ b/content/applications/app_specific/bioinformatics_tools/biodata_module.md
@@ -43,7 +43,7 @@ $ ls $BLAST
 An example of how to run Bowtie2 local alignment on Crane utilizing the default Horse, *Equus caballus* index (*BOWTIE2\_HORSE*) with paired-end fasta files and 8 CPUs is shown below:
 {{% panel header="`bowtie2_alignment.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Bowtie2
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
@@ -64,7 +64,7 @@ bowtie2 -x $BOWTIE2_HORSE -f -1 input_reads_pair_1.fasta -2 input_reads_pair_2.f
 An example of BLAST run against the non-redundant nucleotide database available on Crane is provided below:
 {{% panel header="`blastn_alignment.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=BlastN
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
diff --git a/content/applications/app_specific/bioinformatics_tools/data_manipulation_tools/bamtools/running_bamtools_commands.md b/content/applications/app_specific/bioinformatics_tools/data_manipulation_tools/bamtools/running_bamtools_commands.md
index 07a0275202f5beb0fef6cd85f1d80366fb70cdf3..8cc866a115b4539431844243c82f6671b56b87f9 100644
--- a/content/applications/app_specific/bioinformatics_tools/data_manipulation_tools/bamtools/running_bamtools_commands.md
+++ b/content/applications/app_specific/bioinformatics_tools/data_manipulation_tools/bamtools/running_bamtools_commands.md
@@ -19,7 +19,7 @@ where the option **-format** specifies the type of the output file, **input_a
 Running BamTools **convert** on Crane with input file `input_alignments.bam` and output file `output_reads.fastq` is shown below:
 {{% panel header="`bamtools_convert.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=BamTools_Convert
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=1
diff --git a/content/applications/app_specific/bioinformatics_tools/data_manipulation_tools/samtools/running_samtools_commands.md b/content/applications/app_specific/bioinformatics_tools/data_manipulation_tools/samtools/running_samtools_commands.md
index ac5c097afed0a7b36182b6dba3f748027efd0fe9..9e84ab36c0b84aea6a07d15e78e7367e40b82858 100644
--- a/content/applications/app_specific/bioinformatics_tools/data_manipulation_tools/samtools/running_samtools_commands.md
+++ b/content/applications/app_specific/bioinformatics_tools/data_manipulation_tools/samtools/running_samtools_commands.md
@@ -17,7 +17,7 @@ where **input_alignments.[bam|sam]** is the input file with the alignments in BA
 Running **samtools view** on Crane with `8 CPUs`, input file `input_alignments.sam` with available header (**-S**), output in BAM format (**-b**) and output file `output_alignments.bam` is shown below:
 {{% panel header="`samtools_view.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=SAMtools_View
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
diff --git a/content/applications/app_specific/bioinformatics_tools/data_manipulation_tools/sratoolkit.md b/content/applications/app_specific/bioinformatics_tools/data_manipulation_tools/sratoolkit.md
index d2704b9f8f319a03e749e482c0a137dcd6edbe6d..250963fff0bec0979bea53250af124889cff769c 100644
--- a/content/applications/app_specific/bioinformatics_tools/data_manipulation_tools/sratoolkit.md
+++ b/content/applications/app_specific/bioinformatics_tools/data_manipulation_tools/sratoolkit.md
@@ -21,7 +21,7 @@ $ fastq-dump [options] input_reads.sra
 An example of running **fastq-dump** on Crane to convert SRA file containing paired-end reads is:
 {{% panel header="`sratoolkit.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=SRAtoolkit
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=1
diff --git a/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/oases.md b/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/oases.md
index 82278e8858fb1b26ea367756a8e1e98ab062e929..144583834436bb528ea8da9b98e42473fe6be4e9 100644
--- a/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/oases.md
+++ b/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/oases.md
@@ -28,7 +28,7 @@ Oases has a lot of parameters that can be found in its [manual](https://www.ebi.
 A simple SLURM script to run Oases on the Velvet output stored in `output_directory/` with minimum transcript length of `200` is shown below:
 {{% panel header="`oases.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Velvet_Oases
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=1
diff --git a/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/ray.md b/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/ray.md
index 7e57db1f1d964c035c1cfc2cca6879170bf42cde..99d4f63be823a392599be042f4bda1a8a3fe7a78 100644
--- a/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/ray.md
+++ b/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/ray.md
@@ -41,7 +41,7 @@ Ray supports odd values for k-mer equal to or greater than 21 (`-k <kmer_value>`
 Simple SLURM script for running Ray with both paired-end and single-end data with `k-mer=31`, `8 CPUs` and `4 GB RAM per CPU` is shown below:
 {{% panel header="`ray.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Ray
 #SBATCH --ntasks=8
 #SBATCH --time=168:00:00
diff --git a/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/soapdenovo2.md b/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/soapdenovo2.md
index d4248506b850803365f7207921a62ed533ddd7da..eae39ef874d29f673a650d2dc590ad6611f2585d 100644
--- a/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/soapdenovo2.md
+++ b/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/soapdenovo2.md
@@ -97,7 +97,7 @@ After creating the configuration file **configFile**, the next step is to run th
 Simple SLURM script for running SOAPdenovo2 with `k-mer=31`, `8 CPUSs` and `50GB of RAM` is shown below:
 {{% panel header="`soapdenovo2.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=SOAPdenovo2
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
diff --git a/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/trinity/running_trinity_in_multiple_steps.md b/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/trinity/running_trinity_in_multiple_steps.md
index 086a9ed4b3fc71fdaadf95fa86f370ed8dce7a4b..22fa8383adcd446328cf2e6a354bc5035e77ac13 100644
--- a/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/trinity/running_trinity_in_multiple_steps.md
+++ b/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/trinity/running_trinity_in_multiple_steps.md
@@ -10,7 +10,7 @@ weight = "10"
 The first step of running Trinity is to run Trinity with the option **--no_run_inchworm**:
 {{% panel header="`trinity_step1.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Trinity_Step1
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
@@ -29,7 +29,7 @@ Trinity --seqType fq --max_memory 100G --left input_reads_pair_1.fastq --right i
 The second step of running Trinity is to run Trinity with the option **--no_run_chrysalis**:
 {{% panel header="`trinity_step2.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Trinity_Step2
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
@@ -48,7 +48,7 @@ Trinity --seqType fq --max_memory 100G --left input_reads_pair_1.fastq --right i
 The third step of running Trinity is to run Trinity with the option **--no_distributed_trinity_exec**:
 {{% panel header="`trinity_step3.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Trinity_Step3
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
@@ -67,7 +67,7 @@ Trinity --seqType fq --max_memory 100G --left input_reads_pair_1.fastq --right i
 The fourth step of running Trinity is to run Trinity without any additional option:
 {{% panel header="`trinity_step4.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Trinity_Step4
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
diff --git a/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/velvet/running_velvet_with_paired_end_data.md b/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/velvet/running_velvet_with_paired_end_data.md
index 2f52cc8724f306cc870d700c088f6efcaa4f712e..6e6dc24cadcd6f40c7095065d458d56f1d95e12f 100644
--- a/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/velvet/running_velvet_with_paired_end_data.md
+++ b/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/velvet/running_velvet_with_paired_end_data.md
@@ -10,7 +10,7 @@ weight = "10"
 The first step of running Velvet is to run **velveth**:
 {{% panel header="`velveth.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Velvet_Velveth
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
@@ -30,7 +30,7 @@ velveth output_directory/ 43 -fastq -longPaired -separate input_reads_pair_1.fas
 After running **velveth**, the next step is to run **velvetg** on the `output_directory/` and files generated from **velveth**:
 {{% panel header="`velvetg.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Velvet_Velvetg
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
diff --git a/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/velvet/running_velvet_with_single_end_and_paired_end_data.md b/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/velvet/running_velvet_with_single_end_and_paired_end_data.md
index fa355b11a14273d787bb3eec9703c4d430e20ef8..187e020b00b1ef0d7a91047257821af548cacf67 100644
--- a/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/velvet/running_velvet_with_single_end_and_paired_end_data.md
+++ b/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/velvet/running_velvet_with_single_end_and_paired_end_data.md
@@ -10,7 +10,7 @@ weight = "10"
 The first step of running Velvet is to run **velveth**:
 {{% panel header="`velveth.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Velvet_Velveth
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
@@ -30,7 +30,7 @@ velveth output_directory/ 51 -fasta -short input_reads.fasta -fasta -shortPaired
 After running **velveth**, the next step is to run **velvetg** on the `output_directory/` and files generated from **velveth**:
 {{% panel header="`velvetg.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Velvet_Velvetg
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
diff --git a/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/velvet/running_velvet_with_single_end_data.md b/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/velvet/running_velvet_with_single_end_data.md
index 82efa872ca98a4925e16f0524fe98464130c1997..4528bc6c3ed5f54b0a4b6ba10203e4c3235108ed 100644
--- a/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/velvet/running_velvet_with_single_end_data.md
+++ b/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/velvet/running_velvet_with_single_end_data.md
@@ -10,7 +10,7 @@ weight = "10"
 The first step of running Velvet is to run **velveth**:
 {{% panel header="`velveth.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Velvet_Velveth
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
@@ -30,7 +30,7 @@ velveth output_directory/ 31 -fasta -short input_reads.fasta
 After running **velveth**, the next step is to run **velvetg** on the `output_directory/` and files generated from **velveth**:
 {{% panel header="`velvetg.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Velvet_Velvetg
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
diff --git a/content/applications/app_specific/bioinformatics_tools/pre_processing_tools/cutadapt.md b/content/applications/app_specific/bioinformatics_tools/pre_processing_tools/cutadapt.md
index 6f8770f0b8ab7d2323166d5cb172333ef3d6465b..d0e82b28ba24176240030950c1c94c71ec7517ab 100644
--- a/content/applications/app_specific/bioinformatics_tools/pre_processing_tools/cutadapt.md
+++ b/content/applications/app_specific/bioinformatics_tools/pre_processing_tools/cutadapt.md
@@ -25,7 +25,7 @@ $ cutadapt --help
 Simple Cutadapt script that trims the adapter sequences **AGGCACACAGGG** and **TGAGACACGCA** from the 3' end and **AACCGGTT** from the 5' end of single-end fasta input file is shown below:
 {{% panel header="`cutadapt.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Cutadapt
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=1
diff --git a/content/applications/app_specific/bioinformatics_tools/pre_processing_tools/prinseq.md b/content/applications/app_specific/bioinformatics_tools/pre_processing_tools/prinseq.md
index 09d2fd44d21f6486c08993823090fe8c904eedb3..ea0ad94ee998bf9f7d81dda9ac7e335aa2f28dfc 100644
--- a/content/applications/app_specific/bioinformatics_tools/pre_processing_tools/prinseq.md
+++ b/content/applications/app_specific/bioinformatics_tools/pre_processing_tools/prinseq.md
@@ -27,7 +27,7 @@ The output format (`-out_format`) can be **1** (fasta only), **2** (fasta and qu
 Simple PRINSEQ SLURM script for single-end fasta data and fasta output format is shown below:
 {{% panel header="`prinseq_single_end.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=PRINSEQ
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=1
@@ -59,7 +59,7 @@ The output format (`-out_format`) can be **1** (fasta only), **2** (fasta and qu
 Simple PRINSEQ SLURM script for paired-end fastq data and fastq output format is shown below:
 {{% panel header="`prinseq_paired_end.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=PRINSEQ
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=1
diff --git a/content/applications/app_specific/bioinformatics_tools/pre_processing_tools/scythe.md b/content/applications/app_specific/bioinformatics_tools/pre_processing_tools/scythe.md
index e907b01363814051449e623e54dd8f48ed7a0bad..f19e2bb045d99c632a825ba57ea68c472409e347 100644
--- a/content/applications/app_specific/bioinformatics_tools/pre_processing_tools/scythe.md
+++ b/content/applications/app_specific/bioinformatics_tools/pre_processing_tools/scythe.md
@@ -25,7 +25,7 @@ $ scythe --help
 Simple Scythe script that uses the `illumina_adapters.fa` file and `input_reads.fastq` is shown below:
 {{% panel header="`scythe.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Scythe
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=1
diff --git a/content/applications/app_specific/bioinformatics_tools/pre_processing_tools/sickle.md b/content/applications/app_specific/bioinformatics_tools/pre_processing_tools/sickle.md
index 7550b45007ddef8abed6be6d5a9ad2bc960ef5c4..537264059fd29e724e3abb81da521f2f04e09618 100644
--- a/content/applications/app_specific/bioinformatics_tools/pre_processing_tools/sickle.md
+++ b/content/applications/app_specific/bioinformatics_tools/pre_processing_tools/sickle.md
@@ -28,7 +28,7 @@ where **input_reads.fastq** is the input file of sequencing data in fastq form
 Simple SLURM Sickle script for Illumina single-end reads input file `input_reads.fastq` is shown below:
 {{% panel header="`sickle_single.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Sickle
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=1
@@ -56,7 +56,7 @@ where **input_reads_pair_1.fastq** and **input_reads_pair_2.fastq** are the in
 Simple SLURM Sickle script for Sanger paired-end reads input files `input_reads_pair_1.fastq` and `input_reads_pair_2.fastq` is shown below:
 {{% panel header="`sickle_paired.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Sickle
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=1
diff --git a/content/applications/app_specific/bioinformatics_tools/pre_processing_tools/tagcleaner.md b/content/applications/app_specific/bioinformatics_tools/pre_processing_tools/tagcleaner.md
index eeb9a893dfdf80cfe7493d2b8991118592f4bcd5..6619c5a74d1d71531b2af79ea928da76b30a8a77 100644
--- a/content/applications/app_specific/bioinformatics_tools/pre_processing_tools/tagcleaner.md
+++ b/content/applications/app_specific/bioinformatics_tools/pre_processing_tools/tagcleaner.md
@@ -25,7 +25,7 @@ $ tagcleaner.pl --help
 Simple TagCleaner script for removing known 3' and 5' tag sequences (`NNNCCAAACACACCCAACACA` and `TGTGTTGGGTGTGTTTGGNNN` respectively) is shown below:
 {{% panel header="`tagcleaner.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=TagCleaner
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=1
diff --git a/content/applications/app_specific/bioinformatics_tools/qiime.md b/content/applications/app_specific/bioinformatics_tools/qiime.md
index dfec13f048f5f9e32661e78e3c07f2daf6f42ac2..8d3e2c54a475456e4b3c37a1e75910f8b2358e19 100644
--- a/content/applications/app_specific/bioinformatics_tools/qiime.md
+++ b/content/applications/app_specific/bioinformatics_tools/qiime.md
@@ -35,7 +35,7 @@ Sample QIIME submit script to run **pick_open_reference_otus.py** is:
 
 {{% panel header="`qiime.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=QIIME
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
diff --git a/content/applications/app_specific/bioinformatics_tools/reference_based_assembly_tools/cufflinks.md b/content/applications/app_specific/bioinformatics_tools/reference_based_assembly_tools/cufflinks.md
index 711471e185605e7611dcd1f04abacc6fb65d896f..b48c94f64c0e32bd1c291f4b72e01c9b48a2fa80 100644
--- a/content/applications/app_specific/bioinformatics_tools/reference_based_assembly_tools/cufflinks.md
+++ b/content/applications/app_specific/bioinformatics_tools/reference_based_assembly_tools/cufflinks.md
@@ -22,7 +22,7 @@ $ cufflinks -h
 An example of how to run Cufflinks on Crane with alignment file in SAM format, output directory `cufflinks_output` and 8 CPUs is shown below:
 {{% panel header="`cufflinks.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=Cufflinks
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
diff --git a/content/applications/app_specific/bioinformatics_tools/removing_detecting_redundant_sequences/cap3.md b/content/applications/app_specific/bioinformatics_tools/removing_detecting_redundant_sequences/cap3.md
index c3f17b64c60076f931dbf0a725c393e392da002e..0bc7928e03000ef8f0963e2102c87631d382a6d5 100644
--- a/content/applications/app_specific/bioinformatics_tools/removing_detecting_redundant_sequences/cap3.md
+++ b/content/applications/app_specific/bioinformatics_tools/removing_detecting_redundant_sequences/cap3.md
@@ -21,7 +21,7 @@ An example of how to run basic CAP3 SLURM script on Crane is shown
 below:
 {{% panel header="`cap3.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=CAP3
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=1
diff --git a/content/applications/app_specific/bioinformatics_tools/removing_detecting_redundant_sequences/cd_hit.md b/content/applications/app_specific/bioinformatics_tools/removing_detecting_redundant_sequences/cd_hit.md
index 4fa711fc8dc746afa343a98d56ada2c21b43dc20..c905ce22478a645c1a19dc8a29db61acbc0faeaf 100644
--- a/content/applications/app_specific/bioinformatics_tools/removing_detecting_redundant_sequences/cd_hit.md
+++ b/content/applications/app_specific/bioinformatics_tools/removing_detecting_redundant_sequences/cd_hit.md
@@ -35,7 +35,7 @@ CD-HIT is multi-threaded program, and therefore, using multiple threads is recom
 Simple SLURM CD-HIT script for Crane with 8 CPUs is given in addition:
 {{% panel header="`cd-hit.submit`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=CD-HIT
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
diff --git a/content/applications/app_specific/dmtcp_checkpointing.md b/content/applications/app_specific/dmtcp_checkpointing.md
index 9de1c055fe6790b4d29caea3f04d16b112047bb2..19786d370a6a6e2894b22211d3ca135b0b0c0afd 100644
--- a/content/applications/app_specific/dmtcp_checkpointing.md
+++ b/content/applications/app_specific/dmtcp_checkpointing.md
@@ -66,7 +66,7 @@ on crane is shown below:
 
 {{% panel theme="info" header="dmtcp_blastx.submit" %}}
 {{< highlight batch >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=BlastX
 #SBATCH --nodes=1
 #SBATCH --ntasks=8
@@ -98,7 +98,7 @@ following submit file:
 
 {{% panel theme="info" header="dmtcp_restart_blastx.submit" %}}
 {{< highlight batch >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=BlastX
 #SBATCH --nodes=1
 #SBATCH --ntasks=8
diff --git a/content/applications/app_specific/fortran_c_on_hcc.md b/content/applications/app_specific/fortran_c_on_hcc.md
index 877bd5d0a1752023658c974029264a21a0acaee4..9a2c002f2b20852ef675d1dd8afc7dea0a19812e 100644
--- a/content/applications/app_specific/fortran_c_on_hcc.md
+++ b/content/applications/app_specific/fortran_c_on_hcc.md
@@ -123,7 +123,7 @@ line.
 
 {{% panel header="`submit_f.serial`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --mem-per-cpu=1024
 #SBATCH --time=00:01:00
 #SBATCH --job-name=Fortran
@@ -137,7 +137,7 @@ module load compiler/gcc/4.9
 
 {{% panel header="`submit_c.serial`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --mem-per-cpu=1024
 #SBATCH --time=00:01:00
 #SBATCH --job-name=C
diff --git a/content/applications/app_specific/mpi_jobs_on_hcc.md b/content/applications/app_specific/mpi_jobs_on_hcc.md
index 182012219d5f3e665d097ba3f366238114c06878..5d3792e58017172a33539d85c88fa786355f8a71 100644
--- a/content/applications/app_specific/mpi_jobs_on_hcc.md
+++ b/content/applications/app_specific/mpi_jobs_on_hcc.md
@@ -212,7 +212,7 @@ main program name.
 
 {{% panel header="`submit_f.mpi`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --ntasks=5
 #SBATCH --mem-per-cpu=1024
 #SBATCH --time=00:01:00
@@ -226,7 +226,7 @@ mpirun ./demo_f_mpi.x
 
 {{% panel header="`submit_c.mpi`"%}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --ntasks=5
 #SBATCH --mem-per-cpu=1024
 #SBATCH --time=00:01:00
diff --git a/content/applications/app_specific/running_gaussian_at_hcc.md b/content/applications/app_specific/running_gaussian_at_hcc.md
index 45aa43e6695ea8c60149a1b984a08f85a80508a6..a903fe15e87632a6619be8f30f7f0b17fb383aae 100644
--- a/content/applications/app_specific/running_gaussian_at_hcc.md
+++ b/content/applications/app_specific/running_gaussian_at_hcc.md
@@ -96,7 +96,7 @@ Content of Gaussian SLURM submission file `run-g09-general.slurm`:
 
 {{% panel theme="info" header="run-g09-general.slurm" %}}
 {{< highlight batch >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH -J g09
 #SBATCH --nodes=1 --ntasks-per-node=4
 #SBATCH --mem-per-cpu=2000
@@ -164,7 +164,7 @@ Submit your initial **g09** job with the following SLURM submission file:
 
 {{% panel theme="info" header="Submit with dmtcp" %}}
 {{< highlight batch >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH -J g09-dmtcp
 #SBATCH --nodes=1 --ntasks-per-node=16
 #SBATCH --mem-per-cpu=4000
@@ -214,7 +214,7 @@ resume your interrupted job:
 
 {{% panel theme="info" header="Resume with dmtcp" %}}
 {{< highlight batch >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH -J g09-restart
 #SBATCH --nodes=1 --ntasks-per-node=16
 #SBATCH --mem-per-cpu=4000
diff --git a/content/applications/app_specific/running_ocean_land_atmosphere_model_olam.md b/content/applications/app_specific/running_ocean_land_atmosphere_model_olam.md
index 2efd86d9809458b58df3a384884453df5273a0eb..67dee23d1502bde62ed21e90ee7f9a0b6d51eba9 100644
--- a/content/applications/app_specific/running_ocean_land_atmosphere_model_olam.md
+++ b/content/applications/app_specific/running_ocean_land_atmosphere_model_olam.md
@@ -206,7 +206,7 @@ USE_HDF5=1
 
 {{% panel theme="info" header="Sample submit script for PGI compiler" %}}
 {{< highlight batch >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --ntasks=8                                          # 8 cores
 #SBATCH --mem-per-cpu=1024                                  # Minimum memory required per CPU (in megabytes)
 #SBATCH --time=03:15:00                                     # Run time in hh:mm:ss
@@ -223,7 +223,7 @@ mpirun /path/to/olam-4.2c-mpi
 
 {{% panel theme="info" header="Sample submit script for Intel compiler" %}}
 {{< highlight batch >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --ntasks=8                                          # 8 cores
 #SBATCH --mem-per-cpu=1024                                  # Minimum memory required per CPU (in megabytes)
 #SBATCH --time=03:15:00                                     # Run time in hh:mm:ss
diff --git a/content/applications/user_software/using_singularity.md b/content/applications/user_software/using_singularity.md
index 801f3d628f03b107c4712fea0a6aa41f94d7347e..c5521bf213abf140493ed85681dd33eec25f2920 100644
--- a/content/applications/user_software/using_singularity.md
+++ b/content/applications/user_software/using_singularity.md
@@ -78,7 +78,7 @@ Using Singularity in a SLURM job is similar to how you would use any other softw
 
 {{% panel theme="info" header="Example Singularity SLURM script" %}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --time=03:15:00          # Run time in hh:mm:ss
 #SBATCH --mem-per-cpu=4096       # Maximum memory required per CPU (in megabytes)
 #SBATCH --job-name=singularity-test
@@ -201,7 +201,7 @@ For example,
 
 {{% panel theme="info" header="Example SLURM script" %}}
 {{< highlight bash >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --time=03:15:00          # Run time in hh:mm:ss
 #SBATCH --mem-per-cpu=4096       # Maximum memory required per CPU (in megabytes)
 #SBATCH --job-name=singularity-test
diff --git a/content/submitting_jobs/job_dependencies.md b/content/submitting_jobs/job_dependencies.md
index 36aa971e848093c509eed7076212f6448a338b33..b0dd6b7b32d7068e6f3bf03d1f4fc6d2eb3247c0 100644
--- a/content/submitting_jobs/job_dependencies.md
+++ b/content/submitting_jobs/job_dependencies.md
@@ -34,7 +34,7 @@ The SLURM submit files for each step are below.
 
 {{%expand "JobA.submit" %}}
 {{< highlight batch >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=JobA
 #SBATCH --time=00:05:00
 #SBATCH --ntasks=1
@@ -49,7 +49,7 @@ sleep 120
 
 {{%expand "JobB.submit" %}}
 {{< highlight batch >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=JobB
 #SBATCH --time=00:05:00
 #SBATCH --ntasks=1
@@ -66,7 +66,7 @@ sleep 120
 
 {{%expand "JobC.submit" %}}
 {{< highlight batch >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=JobC
 #SBATCH --time=00:05:00
 #SBATCH --ntasks=1
@@ -83,7 +83,7 @@ sleep 120
 
 {{%expand "JobC.submit" %}}
 {{< highlight batch >}}
-#!/bin/sh
+#!/bin/bash
 #SBATCH --job-name=JobD
 #SBATCH --time=00:05:00
 #SBATCH --ntasks=1