From fde2f4dadb9b24638ca7b99358b78f95ca1b9bae Mon Sep 17 00:00:00 2001
From: Caughlin Bohn <caughlin.bohn@huskers.unl.edu>
Date: Mon, 13 Jul 2020 14:30:33 -0500
Subject: [PATCH] /bin/sh to /bin/bash
---
.../blast_with_allinea_performance_reports.md | 2 +-
.../lammps_with_allinea_performance_reports.md | 2 +-
.../ray_with_allinea_performance_reports.md | 2 +-
.../alignment_tools/blast/create_local_blast_database.md | 2 +-
.../alignment_tools/blast/running_blast_alignment.md | 4 ++--
.../bioinformatics_tools/alignment_tools/blat.md | 2 +-
.../bioinformatics_tools/alignment_tools/bowtie.md | 2 +-
.../bioinformatics_tools/alignment_tools/bowtie2.md | 2 +-
.../alignment_tools/bwa/running_bwa_commands.md | 2 +-
.../bioinformatics_tools/alignment_tools/clustal_omega.md | 2 +-
.../alignment_tools/tophat_tophat2.md | 2 +-
.../app_specific/bioinformatics_tools/biodata_module.md | 4 ++--
.../bamtools/running_bamtools_commands.md | 2 +-
.../samtools/running_samtools_commands.md | 2 +-
.../data_manipulation_tools/sratoolkit.md | 2 +-
.../bioinformatics_tools/de_novo_assembly_tools/oases.md | 2 +-
.../bioinformatics_tools/de_novo_assembly_tools/ray.md | 2 +-
.../de_novo_assembly_tools/soapdenovo2.md | 2 +-
.../trinity/running_trinity_in_multiple_steps.md | 8 ++++----
.../velvet/running_velvet_with_paired_end_data.md | 4 ++--
.../running_velvet_with_single_end_and_paired_end_data.md | 4 ++--
.../velvet/running_velvet_with_single_end_data.md | 4 ++--
.../bioinformatics_tools/pre_processing_tools/cutadapt.md | 2 +-
.../bioinformatics_tools/pre_processing_tools/prinseq.md | 4 ++--
.../bioinformatics_tools/pre_processing_tools/scythe.md | 2 +-
.../bioinformatics_tools/pre_processing_tools/sickle.md | 4 ++--
.../pre_processing_tools/tagcleaner.md | 2 +-
.../app_specific/bioinformatics_tools/qiime.md | 2 +-
.../reference_based_assembly_tools/cufflinks.md | 2 +-
.../removing_detecting_redundant_sequences/cap3.md | 2 +-
.../removing_detecting_redundant_sequences/cd_hit.md | 2 +-
content/applications/app_specific/dmtcp_checkpointing.md | 4 ++--
content/applications/app_specific/fortran_c_on_hcc.md | 4 ++--
content/applications/app_specific/mpi_jobs_on_hcc.md | 4 ++--
.../applications/app_specific/running_gaussian_at_hcc.md | 6 +++---
.../running_ocean_land_atmosphere_model_olam.md | 4 ++--
content/applications/user_software/using_singularity.md | 4 ++--
content/submitting_jobs/job_dependencies.md | 8 ++++----
38 files changed, 58 insertions(+), 58 deletions(-)
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 ec4291ed..d0a891d8 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 cdb77498..eae0db2a 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 28b25aa5..1a21e017 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 4caf0d48..d01dfee4 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 e4de1150..6ed8935c 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 9113bca2..6d41e9c9 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 41aaf03d..ae79a451 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 8d091433..f6054dbf 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 02ad6683..7e96edbc 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 6aeebfae..95b625b2 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 b8047568..c0590f6a 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 c4b7c0a3..97750365 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 07a02752..8cc866a1 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 0a9787f7..c5e5c2f5 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 d2704b9f..250963ff 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 82278e88..14458383 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 7e57db1f..99d4f63b 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 d4248506..eae39ef8 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 086a9ed4..22fa8383 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 2f52cc87..6e6dc24c 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 fa355b11..187e020b 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 82efa872..4528bc6c 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 6f8770f0..d0e82b28 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 09d2fd44..ea0ad94e 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 e907b013..f19e2bb0 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 7550b450..53726405 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 eeb9a893..6619c5a7 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 dfec13f0..8d3e2c54 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 711471e1..b48c94f6 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 c3f17b64..0bc7928e 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 4fa711fc..c905ce22 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 9de1c055..19786d37 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 877bd5d0..9a2c002f 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 18201221..5d3792e5 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 45aa43e6..a903fe15 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 2efd86d9..67dee23d 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 801f3d62..c5521bf2 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 36aa971e..b0dd6b7b 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
--
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