Merge branch 'trinity' into 'master'

Update Trinity version and command

See merge request !228

content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/trinity/_index.md

@@ -10,9 +10,9 @@ weight = "52"
 
 The basic usage of Trinity is:
 {{< highlight bash >}}
-$ Trinity --seqType [fa|fq] --JM <jellyfish_memory> --left input_reads_pair_1.[fa|fq] --right input_reads_pair_2.[fa|fq] [options]
+$ Trinity --seqType [fa|fq] --max_memory <maximum_memory> --left input_reads_pair_1.[fa|fq] --right input_reads_pair_2.[fa|fq] [options]
 {{< /highlight >}}
-where **input_reads_pair_1.[fa|fq]** and **input_reads_pair_2.[fa|fq]** are the input paired-end files of sequence reads in fasta/fastq format, and **--seqType** is the type of these input reads. The option **--JM** defines the number of GB of system memory required for k-mer counting by jellyfish.
+where **input_reads_pair_1.[fa|fq]** and **input_reads_pair_2.[fa|fq]** are the input paired-end files of sequence reads in fasta/fastq format, and **--seqType** is the type of these input reads. The option **--max_memory** specifies the maximum memory to use with Trinity.
 
 Additional Trinity **options** can be found in the Trinity website, or by typing:
 {{< highlight bash >}}

content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/trinity/running_trinity_in_multiple_steps.md

@@ -19,9 +19,9 @@ The first step of running Trinity is to run Trinity with the option **--no_run_c
 #SBATCH --output=Trinity_Step1.%J.out
 #SBATCH --error=Trinity_Step1.%J.err
 
-module load trinity/2.6
+module load trinity
 
-Trinity --seqType fq --JM 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_chrysalis
+Trinity --seqType fq --max_memory 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_chrysalis
 {{< /highlight >}}
 {{% /panel %}}
 
@@ -38,9 +38,9 @@ The second step of running Trinity is to run Trinity with the option **--no_run_
 #SBATCH --output=Trinity_Step2.%J.out
 #SBATCH --error=Trinity_Step2.%J.err
 
-module load trinity/2.6
+module load trinity
 
-Trinity --seqType fq --JM 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_quantifygraph
+Trinity --seqType fq --max_memory 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_quantifygraph
 {{< /highlight >}}
 {{% /panel %}}
 
@@ -57,9 +57,9 @@ The third step of running Trinity is to run Trinity with the option **--no_run_b
 #SBATCH --output=Trinity_Step3.%J.out
 #SBATCH --error=Trinity_Step3.%J.err
 
-module load trinity/2.6
+module load trinity
 
-Trinity --seqType fq --JM 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_butterfly
+Trinity --seqType fq --max_memory 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_butterfly
 {{< /highlight >}}
 {{% /panel %}}
 
@@ -76,9 +76,9 @@ The fourth step of running Trinity is to run Trinity without any additional opti
 #SBATCH --output=Trinity_Step4.%J.out
 #SBATCH --error=Trinity_Step4.%J.err
 
-module load trinity/2.6
+module load trinity
 
-Trinity --seqType fq --JM 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE
+Trinity --seqType fq --max_memory 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE
 {{< /highlight >}}
 {{% /panel %}}