Merge branch 'master' into 'runningSAS'

Fixed Conflicts

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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