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 +1,31 @@
+#! /bin/bash
+set -e
+SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
+MAX_MEMORY=${MAX_MEMORY:-"20G"}
+VIRIDI=${VIRIDI:-"$PROJECTHOME/01.reference/viridiplantae_odb12/"}
+ROSALES=${ROSALES:-"$PROJECTHOME/01.reference/rosales_odb12/"}
+
+if [ "$#" -ne 4 ]; then
+    echo "Usage: $0 <reads_1.fastq> <reads_2.fastq> <stem> <threads>"
+    echo "Perform de novo transcriptome assembly using Trinity"
+    exit 1
+fi
+
+fq1=$1
+fq2=$2
+stem=$3
+outdir="$stem"_trinity_out_dir
+THREADS=$4
+
+
+# Run Trinity for de novo transcriptome assembly
+Trinity --seqType fq --left "$fq1" --right "$fq2" --CPU "$THREADS" --max_memory "$MAX_MEMORY" --output "$outdir"
+# Get Longest isoform per gene
+perl "$SCRIPTS"/trinity_utils/util/misc/get_longest_isoform_seq_per_trinity_gene.pl "$outdir.Trinity.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.fasta" >"$outdir".Trinity.fasta.length_stat.txt
+# Clear temporary directory
+rm -rf "$outdir"
@@ -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
+
@@ -0,0 +1,18 @@
+#! /bin/bash
+set -e
+TMP=${TMP:-"$PROJECTHOME/tmp"}
+
+if [ "$#" -ne 3 ]; then
+    echo "Usage: $0 <transcripts_fasta> <swissprot_database> <output_directory>"
+    echo "Predict coding sequences (CDS) from transcripts using TD2 and MMseqs2"
+    exit 1
+fi
+transcripts=$1
+sprot=$2
+outdir=$3
+
+mkdir -p "$outdir"
+TD2.LongOrfs -t "$transcripts" --precise -@ 8 -O "$outdir"
+mmseqs easy-search "$outdir/longest_orfs.pep" "$sprot" "$outdir/mmseqs.m8" "$TMP" -s 7.0 --threads 16
+TD2.Predict -t "$transcripts" --precise -O "$outdir" --retain-mmseqs-hits "$outdir/mmseqs.m8"
+echo "CDS prediction completed. Results are in $outdir"
@@ -0,0 +1,25 @@
+#! /bin/bash
+set -e
+SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
+
+if [ "$#" -ne 3 ]; then
+    echo "Usage: $0 <input_dir> <output_dir> <extension>"
+    echo "Extract longest isoform per gene and rename sequences"
+    exit 1
+fi
+
+indir=$1
+outdir=$2
+ext=$3
+
+mkdir -p "$outdir"
+# Process each file in the input directory with the specified extension
+for td_cds in "$indir"/*."$ext"; do
+    stem=$(basename "$td_cds" ."$ext")
+    echo "Processing $td_cds($stem) ..."
+    echo "perl $SCRIPTS/trinity_utils/util/misc/get_longest_isoform_seq_per_trinity_gene.pl $td_cds > $outdir/$stem.longest_isoform.fa"
+    perl "$SCRIPTS"/trinity_utils/util/misc/get_longest_isoform_seq_per_trinity_gene.pl "$td_cds" >"$outdir"/"$stem".longest_isoform.fa
+    echo "$SCRIPTS/rename_trinity_fasta.py $outdir/$stem.longest_isoform.fa $stem $outdir/$stem.full_cds.fa"
+    "$SCRIPTS"/miscs/rename_trinity_fasta.py "$outdir"/"$stem".longest_isoform.fa "$stem" "$outdir"/"$stem".full_cds.fa
+    echo "Done."
+done
@@ -0,0 +1,27 @@
+#! /bin/bash
+set -e
+SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
+IDENTITY=${IDENTITY:-0.99}
+THREADS=${THREADS:-6}S
+
+if [ "$#" -ne 3 ]; then
+    echo "Usage: $0 <input_dir> <output_dir> <extension>"
+    echo "Reduce redundancy of CDS files using cd-hit-est"
+    exit 1
+fi
+
+indir=$1
+outdir=$2
+ext=$3
+
+mkdir -p "$outdir"
+# Process each file in the input directory with the specified extension
+for cds in "$indir"/*."$ext"; do
+    stem=$(basename "$cds" ."$ext")
+    echo "Processing $cds($stem) ..."
+    echo "cd-hit-est -i $cds -o $outdir/$stem.cds_rr.fa -c $IDENTITY -n 10 -r 0 -T $THREADS"
+    cd-hit-est -i "$cds" -o "$outdir/$stem".cds_rr.fa -c "$IDENTITY" -n 10 -r 0 -T "$THREADS"
+    echo "seqkit translate $outdir/$stem.cds_rr.fa > $outdir/$stem.prot_rr.fa"
+    seqkit translate "$outdir/$stem".cds_rr.fa >"$outdir/$stem".prot_rr.fa
+    echo "Done."
+done