git: 57d1705819c7 - main - biology/biolibc: Impelled to share/man
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Date: Tue, 23 Jan 2024 14:51:48 UTC
The branch main has been updated by bofh:
URL: https://cgit.FreeBSD.org/ports/commit/?id=57d1705819c717b8291562168b0f7f4948cde663
commit 57d1705819c717b8291562168b0f7f4948cde663
Author: Muhammad Moinur Rahman <bofh@FreeBSD.org>
AuthorDate: 2024-01-23 14:43:57 +0000
Commit: Muhammad Moinur Rahman <bofh@FreeBSD.org>
CommitDate: 2024-01-23 14:51:25 +0000
biology/biolibc: Impelled to share/man
Approved by: portmgr (blanket)
---
biology/biolibc/Makefile | 3 +
biology/biolibc/pkg-plist | 944 +++++++++++++++++++++++-----------------------
2 files changed, 475 insertions(+), 472 deletions(-)
diff --git a/biology/biolibc/Makefile b/biology/biolibc/Makefile
index af8a8764ef5d..954784150868 100644
--- a/biology/biolibc/Makefile
+++ b/biology/biolibc/Makefile
@@ -1,5 +1,6 @@
PORTNAME= biolibc
DISTVERSION= 0.2.6
+PORTREVISION= 1
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org
@@ -16,6 +17,8 @@ USE_LDCONFIG= yes
GH_ACCOUNT= auerlab
+MAKE_ARGS+= MANDIR=${PREFIX}/share/man
+
INSTALL_TARGET= install-strip
pre-build:
diff --git a/biology/biolibc/pkg-plist b/biology/biolibc/pkg-plist
index ef546c985a07..a8b6a302ee2b 100644
--- a/biology/biolibc/pkg-plist
+++ b/biology/biolibc/pkg-plist
@@ -53,475 +53,475 @@ lib/libbiolibc.a
lib/libbiolibc.so
lib/libbiolibc.so.2
lib/libbiolibc.so.2.0
-man/man3/BL_ALIGN_MAX_MISMATCH_PERCENT.3.gz
-man/man3/BL_ALIGN_MIN_MATCH.3.gz
-man/man3/BL_BED_BLOCK_COUNT.3.gz
-man/man3/BL_BED_BLOCK_SIZES.3.gz
-man/man3/BL_BED_BLOCK_SIZES_AE.3.gz
-man/man3/BL_BED_BLOCK_STARTS.3.gz
-man/man3/BL_BED_BLOCK_STARTS_AE.3.gz
-man/man3/BL_BED_CHROM.3.gz
-man/man3/BL_BED_CHROM_AE.3.gz
-man/man3/BL_BED_CHROM_END.3.gz
-man/man3/BL_BED_CHROM_START.3.gz
-man/man3/BL_BED_FIELDS.3.gz
-man/man3/BL_BED_ITEM_RGB.3.gz
-man/man3/BL_BED_ITEM_RGB_AE.3.gz
-man/man3/BL_BED_NAME.3.gz
-man/man3/BL_BED_NAME_AE.3.gz
-man/man3/BL_BED_SCORE.3.gz
-man/man3/BL_BED_STRAND.3.gz
-man/man3/BL_BED_THICK_END.3.gz
-man/man3/BL_BED_THICK_START.3.gz
-man/man3/BL_FASTA_DESC.3.gz
-man/man3/BL_FASTA_DESC_AE.3.gz
-man/man3/BL_FASTA_DESC_ARRAY_SIZE.3.gz
-man/man3/BL_FASTA_DESC_LEN.3.gz
-man/man3/BL_FASTA_SEQ.3.gz
-man/man3/BL_FASTA_SEQ_AE.3.gz
-man/man3/BL_FASTA_SEQ_ARRAY_SIZE.3.gz
-man/man3/BL_FASTA_SEQ_LEN.3.gz
-man/man3/BL_FASTQ_DESC.3.gz
-man/man3/BL_FASTQ_DESC_AE.3.gz
-man/man3/BL_FASTQ_DESC_ARRAY_SIZE.3.gz
-man/man3/BL_FASTQ_DESC_LEN.3.gz
-man/man3/BL_FASTQ_PLUS.3.gz
-man/man3/BL_FASTQ_PLUS_AE.3.gz
-man/man3/BL_FASTQ_PLUS_ARRAY_SIZE.3.gz
-man/man3/BL_FASTQ_PLUS_LEN.3.gz
-man/man3/BL_FASTQ_QUAL.3.gz
-man/man3/BL_FASTQ_QUAL_AE.3.gz
-man/man3/BL_FASTQ_QUAL_ARRAY_SIZE.3.gz
-man/man3/BL_FASTQ_QUAL_LEN.3.gz
-man/man3/BL_FASTQ_SEQ.3.gz
-man/man3/BL_FASTQ_SEQ_AE.3.gz
-man/man3/BL_FASTQ_SEQ_ARRAY_SIZE.3.gz
-man/man3/BL_FASTQ_SEQ_LEN.3.gz
-man/man3/BL_FASTX_FASTA.3.gz
-man/man3/BL_FASTX_FASTQ.3.gz
-man/man3/BL_FASTX_FORMAT.3.gz
-man/man3/BL_FASTX_UNION.3.gz
-man/man3/BL_FASTX_}.3.gz
-man/man3/BL_GFF_ATTRIBUTES.3.gz
-man/man3/BL_GFF_ATTRIBUTES_AE.3.gz
-man/man3/BL_GFF_ATTRIBUTES_ARRAY_SIZE.3.gz
-man/man3/BL_GFF_ATTRIBUTES_LEN.3.gz
-man/man3/BL_GFF_END.3.gz
-man/man3/BL_GFF_FEATURE_ID.3.gz
-man/man3/BL_GFF_FEATURE_ID_AE.3.gz
-man/man3/BL_GFF_FEATURE_NAME.3.gz
-man/man3/BL_GFF_FEATURE_NAME_AE.3.gz
-man/man3/BL_GFF_FEATURE_PARENT.3.gz
-man/man3/BL_GFF_FEATURE_PARENT_AE.3.gz
-man/man3/BL_GFF_FILE_POS.3.gz
-man/man3/BL_GFF_INDEX_ARRAY_SIZE.3.gz
-man/man3/BL_GFF_INDEX_COUNT.3.gz
-man/man3/BL_GFF_INDEX_END.3.gz
-man/man3/BL_GFF_INDEX_END_AE.3.gz
-man/man3/BL_GFF_INDEX_FILE_POS.3.gz
-man/man3/BL_GFF_INDEX_FILE_POS_AE.3.gz
-man/man3/BL_GFF_INDEX_SEQID.3.gz
-man/man3/BL_GFF_INDEX_SEQID_AE.3.gz
-man/man3/BL_GFF_INDEX_START.3.gz
-man/man3/BL_GFF_INDEX_START_AE.3.gz
-man/man3/BL_GFF_PHASE.3.gz
-man/man3/BL_GFF_SCORE.3.gz
-man/man3/BL_GFF_SEQID.3.gz
-man/man3/BL_GFF_SEQID_AE.3.gz
-man/man3/BL_GFF_SOURCE.3.gz
-man/man3/BL_GFF_SOURCE_AE.3.gz
-man/man3/BL_GFF_START.3.gz
-man/man3/BL_GFF_STRAND.3.gz
-man/man3/BL_GFF_TYPE.3.gz
-man/man3/BL_GFF_TYPE_AE.3.gz
-man/man3/BL_OVERLAP_FEATURE1_LEN.3.gz
-man/man3/BL_OVERLAP_FEATURE2_LEN.3.gz
-man/man3/BL_OVERLAP_OVERLAP_END.3.gz
-man/man3/BL_OVERLAP_OVERLAP_LEN.3.gz
-man/man3/BL_OVERLAP_OVERLAP_START.3.gz
-man/man3/BL_POS_LIST_ARRAY_SIZE.3.gz
-man/man3/BL_POS_LIST_COUNT.3.gz
-man/man3/BL_POS_LIST_POSITIONS.3.gz
-man/man3/BL_POS_LIST_POSITIONS_AE.3.gz
-man/man3/BL_SAM_BUFF_ALIGNMENTS.3.gz
-man/man3/BL_SAM_BUFF_ALIGNMENTS_AE.3.gz
-man/man3/BL_SAM_BUFF_BUFFERED_COUNT.3.gz
-man/man3/BL_SAM_BUFF_BUFF_SIZE.3.gz
-man/man3/BL_SAM_BUFF_DISCARDED_ALIGNMENTS.3.gz
-man/man3/BL_SAM_BUFF_DISCARDED_SCORE_SUM.3.gz
-man/man3/BL_SAM_BUFF_DISCARDED_TRAILING.3.gz
-man/man3/BL_SAM_BUFF_INC_DISCARDED_TRAILING.3.gz
-man/man3/BL_SAM_BUFF_INC_TOTAL_ALIGNMENTS.3.gz
-man/man3/BL_SAM_BUFF_INC_TRAILING_ALIGNMENTS.3.gz
-man/man3/BL_SAM_BUFF_MAPQ_HIGH.3.gz
-man/man3/BL_SAM_BUFF_MAPQ_LOW.3.gz
-man/man3/BL_SAM_BUFF_MAPQ_MIN.3.gz
-man/man3/BL_SAM_BUFF_MAPQ_SUM.3.gz
-man/man3/BL_SAM_BUFF_MAX_ALIGNMENTS.3.gz
-man/man3/BL_SAM_BUFF_MAX_COUNT.3.gz
-man/man3/BL_SAM_BUFF_MAX_DISCARDED_SCORE.3.gz
-man/man3/BL_SAM_BUFF_MIN_DISCARDED_SCORE.3.gz
-man/man3/BL_SAM_BUFF_PREVIOUS_POS.3.gz
-man/man3/BL_SAM_BUFF_PREVIOUS_RNAME.3.gz
-man/man3/BL_SAM_BUFF_PREVIOUS_RNAME_AE.3.gz
-man/man3/BL_SAM_BUFF_READS_USED.3.gz
-man/man3/BL_SAM_BUFF_TOTAL_ALIGNMENTS.3.gz
-man/man3/BL_SAM_BUFF_TRAILING_ALIGNMENTS.3.gz
-man/man3/BL_SAM_BUFF_UNMAPPED_ALIGNMENTS.3.gz
-man/man3/BL_SAM_CIGAR.3.gz
-man/man3/BL_SAM_CIGAR_AE.3.gz
-man/man3/BL_SAM_CIGAR_ARRAY_SIZE.3.gz
-man/man3/BL_SAM_CIGAR_LEN.3.gz
-man/man3/BL_SAM_FLAG.3.gz
-man/man3/BL_SAM_MAPQ.3.gz
-man/man3/BL_SAM_PNEXT.3.gz
-man/man3/BL_SAM_POS.3.gz
-man/man3/BL_SAM_QNAME.3.gz
-man/man3/BL_SAM_QNAME_AE.3.gz
-man/man3/BL_SAM_QUAL.3.gz
-man/man3/BL_SAM_QUAL_AE.3.gz
-man/man3/BL_SAM_QUAL_ARRAY_SIZE.3.gz
-man/man3/BL_SAM_QUAL_LEN.3.gz
-man/man3/BL_SAM_RNAME.3.gz
-man/man3/BL_SAM_RNAME_AE.3.gz
-man/man3/BL_SAM_RNEXT.3.gz
-man/man3/BL_SAM_RNEXT_AE.3.gz
-man/man3/BL_SAM_SEQ.3.gz
-man/man3/BL_SAM_SEQ_AE.3.gz
-man/man3/BL_SAM_SEQ_ARRAY_SIZE.3.gz
-man/man3/BL_SAM_SEQ_LEN.3.gz
-man/man3/BL_SAM_TLEN.3.gz
-man/man3/BL_VCF_ALT.3.gz
-man/man3/BL_VCF_ALT_AE.3.gz
-man/man3/BL_VCF_ALT_COUNT.3.gz
-man/man3/BL_VCF_CHROM.3.gz
-man/man3/BL_VCF_CHROM_AE.3.gz
-man/man3/BL_VCF_FILTER.3.gz
-man/man3/BL_VCF_FILTER_AE.3.gz
-man/man3/BL_VCF_FORMAT.3.gz
-man/man3/BL_VCF_FORMAT_AE.3.gz
-man/man3/BL_VCF_FORMAT_ARRAY_SIZE.3.gz
-man/man3/BL_VCF_FORMAT_LEN.3.gz
-man/man3/BL_VCF_ID.3.gz
-man/man3/BL_VCF_ID_AE.3.gz
-man/man3/BL_VCF_INFO.3.gz
-man/man3/BL_VCF_INFO_AE.3.gz
-man/man3/BL_VCF_INFO_ARRAY_SIZE.3.gz
-man/man3/BL_VCF_INFO_LEN.3.gz
-man/man3/BL_VCF_MULTI_SAMPLES.3.gz
-man/man3/BL_VCF_MULTI_SAMPLES_AE.3.gz
-man/man3/BL_VCF_MULTI_SAMPLE_ARRAY_SIZES.3.gz
-man/man3/BL_VCF_MULTI_SAMPLE_ARRAY_SIZES_AE.3.gz
-man/man3/BL_VCF_MULTI_SAMPLE_COUNT.3.gz
-man/man3/BL_VCF_MULTI_SAMPLE_LENS.3.gz
-man/man3/BL_VCF_MULTI_SAMPLE_LENS_AE.3.gz
-man/man3/BL_VCF_MULTI_SAMPLE_POINTER_ARRAY_SIZE.3.gz
-man/man3/BL_VCF_OTHER_COUNT.3.gz
-man/man3/BL_VCF_PHREDS.3.gz
-man/man3/BL_VCF_PHREDS_AE.3.gz
-man/man3/BL_VCF_PHRED_BUFF_SIZE.3.gz
-man/man3/BL_VCF_PHRED_COUNT.3.gz
-man/man3/BL_VCF_POS.3.gz
-man/man3/BL_VCF_QUAL.3.gz
-man/man3/BL_VCF_QUAL_AE.3.gz
-man/man3/BL_VCF_REF.3.gz
-man/man3/BL_VCF_REF_AE.3.gz
-man/man3/BL_VCF_REF_COUNT.3.gz
-man/man3/BL_VCF_SAMPLE_ARRAY_SIZE.3.gz
-man/man3/BL_VCF_SAMPLE_LEN.3.gz
-man/man3/BL_VCF_SAMPLE_MAX.3.gz
-man/man3/BL_VCF_SINGLE_SAMPLE.3.gz
-man/man3/BL_VCF_SINGLE_SAMPLE_AE.3.gz
-man/man3/BL_VCF_SINGLE_SAMPLE_ARRAY_SIZE.3.gz
-man/man3/BL_VCF_SINGLE_SAMPLE_LEN.3.gz
-man/man3/biolibc.3.gz
-man/man3/bl_align_map_seq_exact.3.gz
-man/man3/bl_align_map_seq_sub.3.gz
-man/man3/bl_align_set_max_mismatch_percent.3.gz
-man/man3/bl_align_set_min_match.3.gz
-man/man3/bl_bed_check_order.3.gz
-man/man3/bl_bed_gff3_cmp.3.gz
-man/man3/bl_bed_gff_cmp.3.gz
-man/man3/bl_bed_read.3.gz
-man/man3/bl_bed_set_block_count.3.gz
-man/man3/bl_bed_set_block_sizes.3.gz
-man/man3/bl_bed_set_block_sizes_ae.3.gz
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-man/man3/bl_bed_set_block_starts.3.gz
-man/man3/bl_bed_set_block_starts_ae.3.gz
-man/man3/bl_bed_set_block_starts_cpy.3.gz
-man/man3/bl_bed_set_chrom_ae.3.gz
-man/man3/bl_bed_set_chrom_cpy.3.gz
-man/man3/bl_bed_set_chrom_end.3.gz
-man/man3/bl_bed_set_chrom_start.3.gz
-man/man3/bl_bed_set_fields.3.gz
-man/man3/bl_bed_set_item_rgb_ae.3.gz
-man/man3/bl_bed_set_item_rgb_cpy.3.gz
-man/man3/bl_bed_set_name_ae.3.gz
-man/man3/bl_bed_set_name_cpy.3.gz
-man/man3/bl_bed_set_score.3.gz
-man/man3/bl_bed_set_strand.3.gz
-man/man3/bl_bed_set_thick_end.3.gz
-man/man3/bl_bed_set_thick_start.3.gz
-man/man3/bl_bed_skip_header.3.gz
-man/man3/bl_bed_write.3.gz
-man/man3/bl_chrom_name_cmp.3.gz
-man/man3/bl_fasta_free.3.gz
-man/man3/bl_fasta_init.3.gz
-man/man3/bl_fasta_read.3.gz
-man/man3/bl_fasta_set_desc.3.gz
-man/man3/bl_fasta_set_desc_ae.3.gz
-man/man3/bl_fasta_set_desc_array_size.3.gz
-man/man3/bl_fasta_set_desc_cpy.3.gz
-man/man3/bl_fasta_set_desc_len.3.gz
-man/man3/bl_fasta_set_seq.3.gz
-man/man3/bl_fasta_set_seq_ae.3.gz
-man/man3/bl_fasta_set_seq_array_size.3.gz
-man/man3/bl_fasta_set_seq_cpy.3.gz
-man/man3/bl_fasta_set_seq_len.3.gz
-man/man3/bl_fasta_write.3.gz
-man/man3/bl_fastq_3p_trim.3.gz
-man/man3/bl_fastq_find_3p_low_qual.3.gz
-man/man3/bl_fastq_free.3.gz
-man/man3/bl_fastq_init.3.gz
-man/man3/bl_fastq_name_cmp.3.gz
-man/man3/bl_fastq_read.3.gz
-man/man3/bl_fastq_set_desc.3.gz
-man/man3/bl_fastq_set_desc_ae.3.gz
-man/man3/bl_fastq_set_desc_array_size.3.gz
-man/man3/bl_fastq_set_desc_cpy.3.gz
-man/man3/bl_fastq_set_desc_len.3.gz
-man/man3/bl_fastq_set_plus.3.gz
-man/man3/bl_fastq_set_plus_ae.3.gz
-man/man3/bl_fastq_set_plus_array_size.3.gz
-man/man3/bl_fastq_set_plus_cpy.3.gz
-man/man3/bl_fastq_set_plus_len.3.gz
-man/man3/bl_fastq_set_qual.3.gz
-man/man3/bl_fastq_set_qual_ae.3.gz
-man/man3/bl_fastq_set_qual_array_size.3.gz
-man/man3/bl_fastq_set_qual_cpy.3.gz
-man/man3/bl_fastq_set_qual_len.3.gz
-man/man3/bl_fastq_set_seq.3.gz
-man/man3/bl_fastq_set_seq_ae.3.gz
-man/man3/bl_fastq_set_seq_array_size.3.gz
-man/man3/bl_fastq_set_seq_cpy.3.gz
-man/man3/bl_fastq_set_seq_len.3.gz
-man/man3/bl_fastq_write.3.gz
-man/man3/bl_fastx_desc.3.gz
-man/man3/bl_fastx_desc_len.3.gz
-man/man3/bl_fastx_free.3.gz
-man/man3/bl_fastx_init.3.gz
-man/man3/bl_fastx_plus.3.gz
-man/man3/bl_fastx_plus_len.3.gz
-man/man3/bl_fastx_qual.3.gz
-man/man3/bl_fastx_qual_len.3.gz
-man/man3/bl_fastx_read.3.gz
-man/man3/bl_fastx_seq.3.gz
-man/man3/bl_fastx_seq_len.3.gz
-man/man3/bl_fastx_set_fasta.3.gz
-man/man3/bl_fastx_set_fastq.3.gz
-man/man3/bl_fastx_set_format.3.gz
-man/man3/bl_fastx_write.3.gz
-man/man3/bl_gff3_copy.3.gz
-man/man3/bl_gff3_copy_header.3.gz
-man/man3/bl_gff3_dup.3.gz
-man/man3/bl_gff3_extract_attribute.3.gz
-man/man3/bl_gff3_free.3.gz
-man/man3/bl_gff3_index_add.3.gz
-man/man3/bl_gff3_index_seek_reverse.3.gz
-man/man3/bl_gff3_index_set_array_size.3.gz
-man/man3/bl_gff3_index_set_count.3.gz
-man/man3/bl_gff3_index_set_end.3.gz
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-man/man3/bl_gff3_index_set_file_pos.3.gz
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-man/man3/bl_gff3_index_set_seqid.3.gz
-man/man3/bl_gff3_index_set_seqid_ae.3.gz
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-man/man3/bl_gff3_index_set_start.3.gz
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-man/man3/bl_gff3_init.3.gz
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-man/man3/bl_gff3_sam_cmp.3.gz
-man/man3/bl_gff3_sam_overlap.3.gz
-man/man3/bl_gff3_set_attributes.3.gz
-man/man3/bl_gff3_set_attributes_ae.3.gz
-man/man3/bl_gff3_set_attributes_array_size.3.gz
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-man/man3/bl_gff3_set_feature_id.3.gz
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-man/man3/bl_gff3_set_feature_name.3.gz
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-man/man3/bl_gff3_set_feature_parent.3.gz
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-man/man3/bl_gff3_set_feature_parent_cpy.3.gz
-man/man3/bl_gff3_set_file_pos.3.gz
-man/man3/bl_gff3_set_gene_name_cpy.3.gz
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-man/man3/bl_gff3_set_score.3.gz
-man/man3/bl_gff3_set_seqid_ae.3.gz
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-man/man3/bl_gff3_set_source_ae.3.gz
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-man/man3/bl_gff3_set_strand.3.gz
-man/man3/bl_gff3_set_type_ae.3.gz
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-man/man3/bl_pos_list_from_csv.3.gz
-man/man3/bl_pos_list_set_array_size.3.gz
-man/man3/bl_pos_list_set_count.3.gz
-man/man3/bl_pos_list_set_positions.3.gz
-man/man3/bl_pos_list_set_positions_ae.3.gz
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-man/man3/bl_sam_buff_add_alignment.3.gz
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-man/man3/bl_sam_buff_out_of_order.3.gz
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