Add Vercel configuration for rewrites and build settings

2025-12-17 17:47:45 +08:00
parent 072524e303
commit 0d31d42de4
32 changed files with 7435 additions and 289 deletions
@@ -0,0 +1,37 @@
+#! /bin/bash
+set -e
+MAX_MEMORY=${MAX_MEMORY:-"50G"}
+VIRIDI=${VIRIDI:-"$PROJECTHOME/01.reference/viridiplantae_odb12/"}
+ROSALES=${ROSALES:-"$PROJECTHOME/01.reference/rosales_odb12/"}
+SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
+
+if [ "$#" -ne 5 ]; then
+    echo "Usage: $0 <reads_1.fastq> <reads_2.fastq> <ref> <stem> <threads>"
+    echo "Perform reference-guided transcriptome assembly using Hisat2 and Trinity"
+    exit 1
+fi
+
+fq1=$1
+fq2=$2
+ref=$3
+stem=$4
+outdir="$stem"_trinity_out_dir
+THREADS=$5
+
+
+# Run Hisat2 for reads mapping to reference genome
+hisat2 -p "$THREADS" --dta -x "$ref" -1 "$fq1" -2 "$fq2" -S "$stem".sam
+samtools view -b -@ "$THREADS" -o "$stem".raw.bam "$stem".sam
+samtools sort -@ "$THREADS" -o "$stem".sorted.bam "$stem".raw.bam
+samtools index "$stem".sorted.bam
+rm "$stem".sam "$stem".raw.bam
+# Run Trinity for de novo transcriptome assembly
+Trinity --genome_guided_bam "$stem".sorted.bam --genome_guided_max_intron 10000 --max_memory "$MAX_MEMORY" --CPU "$THREADS" --output "$outdir"
+# Get Longest isoform per gene
+perl "$SCRIPTS"/trinity_utils/util/misc/get_longest_isoform_seq_per_trinity_gene.pl "$outdir/Trinity-GG.fasta" >"$outdir/longest_isoform.fasta"
+# BUSCO assessment
+busco -i "$outdir"/longest_isoform.fasta -l "$VIRIDI" -m tran --cpu "$THREADS" -o "$outdir"/busco_viridi -f
+busco -i "$outdir"/longest_isoform.fasta -l "$ROSALES" -m tran --cpu "$THREADS" -o "$outdir"/busco_rosales -f
+# Length Statistics
+TrinityStats.pl "$outdir"/Trinity-GG.fasta >"$outdir"/length_stat.txt
+