sed+awk+Rscript

最新推荐文章于 2025-09-10 01:54:33 发布
原创 最新推荐文章于 2025-09-10 01:54:33 发布 · 135 阅读 · 0 ·
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这篇博客介绍了如何使用Linux命令行工具sed和awk对数据进行预处理，然后通过R脚本进行统计分析，包括计算平均值、中位数、四分位数等，并探讨了这些工具在数据分析中的应用。 
cat ... | sed "s,.*latency:\([0-9]*\) num:\([0-9]\).*,\1 \2,g" | awk '{tm=$1; num=$2; tmSum=tmSum+tm; if(num>0) {print tmSum/num; tmSum=0;} }' | 

Rscript -e 'marr=as.numeric (readLines ("stdin")) ; summary(marr); cat("length:"); length(marr); cat("var-sd:"); sd(marr); quantile(marr,c(0.25,0.5,0.75,0.95,0.99))'
Rscript -e 'marr=as.numeric (readLines ("stdin")) ; summary(marr); cat("  长度"); length(marr); cat("标准差"); var(marr); cat("  方差"); sd(marr)'
顺式元件热图+柱状图
BioinfoDu
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启动子是DNA序列，可以被RNA 聚合酶识别、与其结合从而开始转录，它含有RNA 聚合酶特异性结合和转录起始所需的保守序列，多数位于结构基因转录起始点的上游,启动子本身不被转录。启动子的特性最初是通过能增加或降低基因转录速率的突变而鉴定的。登录网站：（http://bioinformatics.psb.ugent.be/webtools/plantcare/html/)，提交提取的启动子序列和邮箱号，预测结束后会将结果（plantCARE_output_PlantCARE_*.tab文件）发至邮箱。
GWAS全基因组关联分析实战——基于Plink转换vcf数据为二进制
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vcf数据是保存变异信息的主要数据格式，plink是进行全基因组关联分析（GWAs）分析的常用工具包，同时提供一系列数据转换、裁剪和遗传统计量计算工具。本文以实际数据提供基因组关联分析方法。
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DADA2+Kraken2分析16s之细菌   DADA2在QIIME2中是以命令行形式呈现，有时候我们不想装QIIME2，但又想用命令行来运行DADA2。那可咋搞？我们可自己封装R代码为命令行，这个方式对于不熟悉代码的人来说效率比较低，我们可以从QIIME2里面把对应的DADA2运行的代码抠出来，点击我即可链接到地址；我们可以看到有run_dada_paired.R和run_dada_single.R两个文件，根据自己需要下载即可，这里以run_dada_paired.R为例。下载后，我们需要修改命令行传
在shell中直接调用使用R
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shell、R工作流兼容的1个补充
EasyAmplicon (易扩增子)-扩增子高通量序列分析软件流程及脚本-详细使用方法——来自刘永鑫团队的秘籍
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先按照大神自己的实验设计描述整理一个全信息的表格，表头设置为一样，这里就不解释字段意思了，会实验设计的基本都了解，样例文件在EasyAmplicon/result下，大家同样整理一个名为metadata_raw.txt的文件放入新的work文件夹。# -a 找不到输入列将终止运行（默认不执行）-c 将整数列转换为factor或具有小数点的数字，-t 偏离提示标签时转换ID列，-w 颜色带，区域宽度等， -D输出目录，-i OTU列名，-l OTU显示名称如种/属/科名，
linux统计分析命令datamash
刘永鑫的博客——宏基因组公众号
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文章目录引子datamash 是什么调用格式与参数主要 operationPrimary operations:Line-Filtering operations:Per-Line operations:Group-by Numeric operations:Group-by Textual/Numeric operations:**主要参数**操作示例文本基本操作分组统计操作生信相关文本基因表达...
(17) CAFE之后的特异节点基因家族富集分析
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基因富集分析，加油加油
数据清洗革命：用AI驱动的ShellGPT实现原始数据自动化处理
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你是否还在为杂乱无章的原始数据头疼？手动编写正则表达式、处理缺失值、转换数据格式，这些重复性工作不仅耗时耗力，还容易出错。作为数据分析师，你可能每天要花费40%以上的时间在数据准备阶段；作为开发人员，你可能需要为不同数据源编写定制化的清洗脚本。现在，有了ShellGPT（Shell-powered GPT）这一命令行生产力工具，你可以利用AI的力量自动化完成这些繁琐的数据清洗任务。 读完本文，你...
seqminopt matlab,AR_Chip-seq数据分析
weixin_27064205的博客
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#质控cd /home/train/Liuping/raw_data/fastq_filefastqc -t 32 -o /home/train/Liuping/raw_data/fastq_file/fastqc_raw/ /home/train/Liuping/raw_data/fastq_file/*.fastq#去接头java -jar /opt/biosoft/Trimmomatic-0...
批量运行免疫浸润工具：Shell+Perl协同脚本设计的5种高效模式（提升效率10倍）
!... # 摘要 免疫浸润分析在肿瘤微环境研究中具有重要意义，但其多工具、大批量的特性对自动化处理提出了迫切需求。本文系统阐述了Shell与Perl脚本在免疫浸润全流程中的协同应用，提出五种高效集成模式，涵盖任务调度...
merge1：gene SX1-1 SX1-2 SX1-3 SX2-1 SX2-2 SX2-3 SX3-1 SX3-2 SX3-3 BX1-1 BX1-2 BX1-3 BX2-1 BX2-2 BX2-3 BX3-1 BX3-2 BX3-3 SC1-1 SC1-2 SC1-3 SC2-1 SC2-2 SC2-3 SC3-1 SC3-2 SC3-3 XH1-1 XH1-2 XH1-3 XH2-1 XH2-2 XH2-3 XH3-1 XH3-2 XH3-3；sx1 vs sx2， sx1 vs sx3，sx2 vs sx3，bx1 vs bx2，bx1 vs bx 3, bx2 vs bx3,sc1 vs sc2,sc1 vs sc3,sc2 vs sc3,xh1 vs xh2,xh1 vs xh 3,xh2 vs xh3；sx1 vs bx1,sx1 vs sc1,sx1 vs xh1,以此类推；merge2.count同样按照这个逻辑进行分割比较；按章以上要求更改代码：cut -f 1,2,3,4,5,6,7 merge2.count |sed '1s/.*/Symbol\tA\tA\tA\tB\tB\tB/' >CH1_GB.count Rscript edgeR_rep3.R CH1_GB.count CH1_GB.count.DE python de_up_down.py CH1_GB.count CH1_GB.count.DE 2 0.01 gene_anno.txt >CH1_GB.count.DE.fillter ################### cut -f 1,2,3,4,8,9,10 merge2.count |sed '1s/.*/Symbol\tA\tA\tA\tB\tB\tB/' >CH2_GB.count Rscript edgeR_rep3.R CH2_GB.count CH2_GB.count.DE python de_up_down.py CH2_GB.count CH2_GB.count.DE 2 0.01 gene_anno.txt >CH2_GB.count.DE.fillter ################### cut -f 1,2,3,4,11,12,13 merge2.count |sed '1s/.*/Symbol\tA\tA\tA\tB\tB\tB/' >CH3_GB.count Rscript edgeR_rep3.R CH3_GB.count CH3_GB.count.DE python de_up_down.py CH3_GB.count CH3_GB.count.DE 2 0.01 gene_anno.txt >CH3_GB.count.DE.fillter
06-05
Rscript edgeR_rep3.R -i ${comp_name}.count -g ${comp_name}_groups.txt -o ${comp_name}_edgeR # 步骤3: 执行差异表达分析 python de_up_down.py -i ${comp_name}_edgeR.csv -c "${group1}_vs_${group2}" ...
linux如何读取CSV文件并处理其内容
11-30
其中最常用的工具有`cat`, `cut`, `grep`, `awk`, 和 `sed`。以下是一个简单的流程： 1. **查看文件内容**： ``` cat filename.csv ``` 2. **基本分割和过滤**： - 使用`cut`提取特定列： ``` cut -d',' -f1...
#!/bin/bash rm -rf buildroot/output/rockchip_rv1126b/build/deviceTest-1.0/ if [ -z "$BASH_SOURCE" ]; then echo "Not in bash, switching to it..." case "${@:-shell}" in shell) ./build.sh shell ;; *) ./build.sh $@ bash ;; esac fi usage_clean() { usage_oneline "cleanall" "cleanup all" for s in $(grep -rwl clean_hook "$RK_CHIP_SCRIPTS_DIR" \ "$RK_SCRIPTS_DIR" 2>/dev/null | grep "/mk-" | \ sed "s/^.*mk-\(.*\).sh/\1/" | grep -v "^all$"); do usage_oneline "clean-$s" "cleanup $s" done } usage() { echo "Usage: $(basename $BASH_SOURCE) [OPTIONS]" echo "Available options:" run_build_hooks usage # Global options usage_clean usage_oneline "post-rootfs <rootfs dir>" "trigger post-rootfs hook scripts" usage_oneline "help" "display this information" echo "" echo "Default option is '$RK_DEFAULT_TARGET'." rm -f "$INITIAL_ENV" exit 0 } # Export global functions set -a rk_log() { LOG_COLOR="$1" shift if [ "$1" = "-n" ]; then shift LOG_FLAG="-ne" else LOG_FLAG="-e" fi echo $LOG_FLAG "\e[${LOG_COLOR}m$@\e[0m" } message() { rk_log 36 "$@" # light blue } notice() { rk_log 35 "$@" # purple } warning() { rk_log 34 "$@" # dark blue } error() { rk_log 91 "$@" # light red } fatal() { rk_log 31 "$@" # dark red } usage_oneline() { printf "%-40s%s\n" "$1" "${*:2}" } usage_makefile_oneline() { printf " %-22s - %s\n" "$(echo "$1" | grep -o "^[^[^:^ ]*")" "${*:2}" } finish_build() { notice "Running $(basename "${BASH_SOURCE[1]}") - ${@:-${FUNCNAME[1]}} succeeded." cd "$RK_SDK_DIR" } load_config() { [ -r "$RK_CONFIG" ] || return 0 for var in $@; do export "$(grep "^$var=" "$RK_CONFIG" | tr -d '"' || true)" \ &>/dev/null || true done } check_config() { unset missing for var in $@; do eval [ -z \"\$$var\" ] || continue missing="$missing $var" done [ "$missing" ] || return 0 notice "Skipping $(basename "${BASH_SOURCE[1]}") - ${FUNCNAME[1]} for missing configs: $missing." return 1 } kernel_version_raw() { [ -d kernel ] || return 0 VERSION_KEYS="VERSION PATCHLEVEL" VERSION="" for k in $VERSION_KEYS; do v=$(grep "^$k = " kernel/Makefile | cut -d' ' -f3) VERSION=${VERSION:+${VERSION}.}$v done echo $VERSION } kernel_version() { [ -d kernel ] || return 0 KERNEL_DIR="$(basename "$(realpath kernel)")" case "$KERNEL_DIR" in kernel-*) echo ${KERNEL_DIR#kernel-} return 0 ;; esac kernel_version_raw } start_log() { LOG_FILE="$RK_LOG_DIR/${2:-$1_$(date +%F_%H-%M-%S)}.log" ln -rsf "$LOG_FILE" "$RK_LOG_DIR/$1.log" echo "# $(date +"%F %T")" >> "$LOG_FILE" echo "$LOG_FILE" } get_toolchain() { MODULE="$1" TC_ARCH="${2/arm64/aarch64}" TC_VENDOR="${3-none}" TC_OS="${4:-linux}" MACHINE=$(uname -m) if [ "$MACHINE" != x86_64 ]; then notice "Using Non-x86 toolchain for $MODULE!" >&2 if [ "$TC_ARCH" = aarch64 -a "$MACHINE" != aarch64 ]; then echo aarch64-linux-gnu- elif [ "$TC_ARCH" = arm -a "$MACHINE" != armv7l ]; then echo arm-linux-gnueabihf- fi return 0 fi # RV1126 uses custom toolchain if [ "$RK_CHIP_FAMILY" = "rv1126_rv1109" ]; then TC_VENDOR=rockchip830 fi TC_DIR="$RK_SDK_DIR/prebuilts/gcc/linux-x86/$TC_ARCH" if [ "$TC_VENDOR" ]; then TC_PATTERN="$TC_ARCH-$TC_VENDOR-$TC_OS-[^-]*-gcc" else TC_PATTERN="$TC_ARCH-$TC_OS-[^-]*-gcc" fi GCC="$(find "$TC_DIR" -name "*gcc" | grep -m 1 "/$TC_PATTERN$" || true)" if [ ! -x "$GCC" ]; then { error "No prebuilt GCC toolchain for $MODULE!" error "Arch: $TC_ARCH" error "Vendor: $TC_VENDOR" error "OS: $TC_OS" } >&2 exit 1 fi echo ${GCC%gcc} } ensure_tools() { for t in "$@"; do if [ "$RK_ROOTFS_PREFER_PREBUILT_TOOLS" ] || \ [ "$RK_ROOTFS_PREBUILT_TOOLS" ] || \ [ ! -e "$t" ]; then install -v -D -m 0755 "$RK_TOOLS_DIR/armhf/${t##*/}" "$t" continue fi if [ ! -e "$t" ]; then warning "Unable to install $t!" fi done } # For developing shell only rroot() { cd "$RK_SDK_DIR" } rout() { cd "$RK_OUTDIR" } rcommon() { cd "$RK_COMMON_DIR" } rscript() { cd "$RK_SCRIPTS_DIR" } rchip() { cd "$(realpath "$RK_CHIP_DIR")" } set +a # End of global functions err_handler() { ret=${1:-$?} if [ "$ret" -eq 0 ]; then return 0 fi fatal "ERROR: Running $BASH_SOURCE - ${2:-${FUNCNAME[1]}} failed!" fatal "ERROR: exit code $ret from line ${BASH_LINENO[0]}:" fatal " ${3:-$BASH_COMMAND}" fatal "ERROR: call stack:" for i in $(seq 1 $((${#FUNCNAME[@]} - 1))); do SOURCE="${BASH_SOURCE[$i]}" LINE=${BASH_LINENO[$(( $i - 1 ))]} fatal " $(basename "$SOURCE"): ${FUNCNAME[$i]}($LINE)" done exit $ret } # option_check "<supported commands>" <option 1> [option 2] ... option_check() { CMDS="$1" shift for opt in $@; do for cmd in $CMDS; do # NOTE: There might be patterns in commands if echo "${opt%%:*}" | grep -qE "^$cmd$"; then return 0 fi done done return 1 } # hook_check <hook> <stage> <cmd> hook_check() { case "$2" in init | pre-build | build | post-build) ;; *) return 0 ;; esac SCRIPT="$(realpath "$1" --relative-to "$RK_SDK_DIR")" CMDS="$(sed -n \ "s@^RK_${2//-/_}_CMDS[^ ]*\(.*\)\" # $SCRIPT\$@\1@ip" \ "$RK_PARSED_CMDS")" if echo "$CMDS" | grep -wq default; then return 0 fi option_check "$CMDS" "$3" } # Run specific hook scripts do_run_hooks() { HOOK_DIR="$1" shift [ -d "$HOOK_DIR" ] || return 0 for hook in $(find "$HOOK_DIR" -maxdepth 1 -name "*.sh" | sort); do # Ignore unrelated hooks hook_check "$hook" "$@" || continue if "$hook" "$@"; then continue else HOOK_RET=$? err_handler $HOOK_RET \ "${FUNCNAME[0]} $*" "$hook $*" exit $HOOK_RET fi done } run_hooks() { case "${2:-usage}" in usage) do_run_hooks "$RK_COMMON_DIR/$1" "${@:2}" do_run_hooks "$RK_CHIP_DIR/$1" "${@:2}" ;; *) # Prefer chips' hooks than the common ones do_run_hooks "$RK_CHIP_DIR/$1" "${@:2}" do_run_hooks "$RK_COMMON_DIR/$1" "${@:2}" ;; esac } # Run build hook scripts for normal stages run_build_hooks() { # Don't log these stages (either interactive or with useless logs) case "$1" in init | pre-build | make-* | usage | parse-cmds) run_hooks "$RK_BUILD_HOOK_DIR" "$@" || true return 0 ;; esac LOG_FILE="$(start_log "$1")" echo -e "# run hook: $@\n" >> "$LOG_FILE" run_hooks "$RK_BUILD_HOOK_DIR" "$@" 2>&1 | tee -a "$LOG_FILE" HOOK_RET=${PIPESTATUS[0]} if [ $HOOK_RET -ne 0 ]; then err_handler $HOOK_RET "${FUNCNAME[0]} $*" "$@" exit $HOOK_RET fi } # Run post hook scripts for post-rootfs stage run_post_hooks() { LOG_FILE="$(start_log post-rootfs)" echo -e "# run hook: $@\n" >> "$LOG_FILE" run_hooks "$RK_POST_HOOK_DIR" "$@" 2>&1 | tee -a "$LOG_FILE" HOOK_RET=${PIPESTATUS[0]} if [ $HOOK_RET -ne 0 ]; then err_handler $HOOK_RET "${FUNCNAME[0]} $*" "$@" exit $HOOK_RET fi } setup_environments() { export LC_ALL=C export RK_SCRIPTS_DIR="$(dirname "$(realpath "$BASH_SOURCE")")" export RK_COMMON_DIR="$(realpath "$RK_SCRIPTS_DIR/..")" export RK_SDK_DIR="$(realpath "$RK_COMMON_DIR/../../..")" export RK_DEVICE_DIR="$RK_SDK_DIR/device/rockchip" export RK_CHIPS_DIR="$RK_DEVICE_DIR/.chips" export RK_CHIP_DIR="$RK_DEVICE_DIR/.chip" export RK_CHIP_SCRIPTS_DIR="$RK_CHIP_DIR/scripts" export RK_DEFAULT_TARGET="all" export RK_DATA_DIR="$RK_COMMON_DIR/data" export RK_TOOLS_DIR="$RK_COMMON_DIR/tools" export RK_EXTRA_PARTS_DIR="$RK_COMMON_DIR/extra-parts" export RK_KBUILD_DIR="$RK_COMMON_DIR/linux-kbuild" export RK_CONFIG_IN="$RK_COMMON_DIR/configs/Config.in" export RK_BUILD_HOOK_DIR="build-hooks" export RK_POST_HOOK_DIR="post-hooks" export RK_BUILD_HELPER="$RK_SCRIPTS_DIR/build-helper" export RK_POST_HELPER="$RK_SCRIPTS_DIR/post-helper" export RK_PARTITION_HELPER="$RK_SCRIPTS_DIR/partition-helper" export RK_OUTDIR="$RK_SDK_DIR/output" export RK_EXTRA_PART_OUTDIR="$RK_OUTDIR/extra-parts" export RK_SESSION_DIR="$RK_OUTDIR/sessions" export RK_SESSION="${RK_SESSION:-$(date +%F_%H-%M-%S)}" export RK_LOG_DIR="$RK_SESSION_DIR/$RK_SESSION" export RK_LOG_BASE_DIR="$RK_OUTDIR/log" export RK_ROCKDEV_DIR="$RK_SDK_DIR/rockdev" export RK_FIRMWARE_DIR="$RK_OUTDIR/firmware" export RK_CONFIG="$RK_OUTDIR/.config" export RK_DEFCONFIG_LINK="$RK_OUTDIR/defconfig" export RK_OWNER="$(stat --format %U "$RK_SDK_DIR")" export RK_OWNER_UID="$(stat --format %u "$RK_SDK_DIR")" RK_PARSED_CMDS="$RK_OUTDIR/.parsed_cmds" RK_MAKE_USAGE="$RK_OUTDIR/.make_usage" } check_sdk() { if ! echo "$RK_SCRIPTS_DIR" | \ grep -q "device/rockchip/common/scripts$"; then fatal "SDK corrupted!" error "Running $BASH_SOURCE from $RK_SCRIPTS_DIR:" ls --file-type "$RK_SCRIPTS_DIR" exit 1 fi "$RK_SCRIPTS_DIR/check-sdk.sh" # Detect sudo(root) unset RK_SUDO_ROOT if [ "$RK_OWNER_UID" -ne 0 ] && [ "${USER:-$(id -un)}" = "root" ]; then export RK_SUDO_ROOT=1 notice "Running within sudo(root) environment!" echo fi } parse_scripts() { mkdir -p "$RK_OUTDIR" if [ ! -r "$RK_MAKE_USAGE" ] || \ [ "$(find "$RK_SCRIPTS_DIR" "$RK_CHIP_DIR" "$RK_CHIP_DIR/" \ -cnewer "$RK_MAKE_USAGE" 2>/dev/null)" ]; then { TEMP_FILE=$(mktemp -u) for c in $(ls "$RK_CHIPS_DIR"); do usage_makefile_oneline "$c" "choose $c" done > $TEMP_FILE run_build_hooks make-usage >> $TEMP_FILE usage_clean | \ while read LINE; do usage_makefile_oneline $LINE done >> $TEMP_FILE mv $TEMP_FILE "$RK_MAKE_USAGE" }& fi if [ ! -r "$RK_PARSED_CMDS" ] || \ [ "$(find "$RK_SCRIPTS_DIR" "$RK_CHIP_DIR" "$RK_CHIP_DIR/" \ -cnewer "$RK_PARSED_CMDS" 2>/dev/null)" ]; then { TEMP_FILE=$(mktemp -u) { echo "#!/bin/bash" run_build_hooks parse-cmds } > $TEMP_FILE mv $TEMP_FILE "$RK_PARSED_CMDS" }& fi wait } makefile_options() { unset DEBUG setup_environments check_sdk >&2 || exit 1 parse_scripts case "$1" in make-usage) cat "$RK_MAKE_USAGE" ;; make-targets) cat "$RK_MAKE_USAGE" | awk '{print $1}' ;; esac exit 0 } main() { # Early handler of Makefile options case "$@" in make-*) makefile_options $@ ;; esac [ -z "$DEBUG" ] || set -x trap 'err_handler' ERR set -eE # Save intial envionments unset INITIAL_SESSION INITIAL_ENV=$(mktemp -u) env > "$INITIAL_ENV" [ "$RK_SESSION" ] || INITIAL_SESSION=1 # Setup basic environments setup_environments # Log SDK information MANIFEST="$RK_SDK_DIR/.repo/manifest.xml" if [ -e "$MANIFEST" ]; then if [ ! -L "$MANIFEST" ]; then MANIFEST="$RK_SDK_DIR/.repo/manifests/$(grep -o "[^\"]*\.xml" "$MANIFEST")" fi TAG="$(grep -o "linux-.*-gen-rkr[^.\"]*" "$MANIFEST" | \ head -n 1 || true)" MANIFEST="$(basename "$(realpath "$MANIFEST")")" notice "\n############### Rockchip Linux SDK ###############\n" notice "Manifest: $MANIFEST" if [ "$TAG" ]; then notice "Version: $TAG" fi echo fi notice -n "Log colors: " message -n "message " notice -n "notice " warning -n "warning " error -n "error " fatal "fatal" echo # Check SDK requirements check_sdk # Check for session validation if [ -z "$INITIAL_SESSION" ] && [ ! -d "$RK_LOG_DIR" ]; then warning "Session($RK_SESSION) is invalid!" export RK_SESSION="$(date +%F_%H-%M-%S)" export RK_LOG_DIR="$RK_SESSION_DIR/$RK_SESSION" INITIAL_SESSION=1 fi export RK_INITIAL_ENV="$RK_LOG_DIR/initial.env" export RK_CUSTOM_ENV="$RK_LOG_DIR/custom.env" export RK_FINAL_ENV="$RK_LOG_DIR/final.env" mkdir -p "$RK_FIRMWARE_DIR" cd "$RK_SDK_DIR" [ -f README.md ] || ln -rsf "$RK_COMMON_DIR/README.md" . [ -d common ] || ln -rsf "$RK_COMMON_DIR" . # TODO: Remove it in the repo manifest.xml rm -f envsetup.sh OPTIONS="${@:-$RK_DEFAULT_TARGET}" # Special handle for chip and defconfig # e.g. ./build.sh rk3588:rockchip_defconfig for opt in $OPTIONS; do if [ -d "$RK_CHIPS_DIR/${opt%%:*}" ]; then OPTIONS=$(echo "$OPTIONS" | xargs -n 1 | \ sed "s/^$opt$/chip:$opt/" | xargs) elif echo "$opt" | grep -q "^[0-9a-z_]*_defconfig$"; then OPTIONS=$(echo "$OPTIONS" | xargs -n 1 | \ sed "s/^$opt$/defconfig:$opt/" | xargs) fi done # Parse supported commands parse_scripts source "$RK_PARSED_CMDS" # For rpdzkj link init to chip option if [ "$OPTIONS" = "init" ]; then OPTIONS=chip fi # Options checking CMDS="$RK_INIT_CMDS $RK_PRE_BUILD_CMDS $RK_BUILD_CMDS \ $RK_POST_BUILD_CMDS" for opt in $OPTIONS; do case "$opt" in help | h | -h | --help | usage | \?) usage ;; clean-*) # Check cleanup module MODULE="$(echo ${opt#clean-})" grep -wq clean_hook \ "$RK_SCRIPTS_DIR/mk-$MODULE.sh" \ "$RK_CHIP_SCRIPTS_DIR/mk-$MODULE.sh" \ 2>/dev/null || usage ;& shell | buildroot-shell | bshell | cleanall) # Check single options if [ "$opt" = "$OPTIONS" ]; then break fi error "ERROR: $opt cannot combine with other options!" ;; post-rootfs) if [ "$opt" = "$1" -a -d "$2" ]; then # Hide args from later checks OPTIONS=$opt break fi error "ERROR: $opt should be the first option followed by rootfs dir!" ;; *) # Make sure that all options are handled if option_check "$CMDS" $opt; then continue fi error "ERROR: Unhandled option: $opt" ;; esac usage done # Prepare log dirs if [ ! -d "$RK_LOG_DIR" ]; then rm -rf "$RK_LOG_BASE_DIR" "$RK_LOG_DIR" "$RK_SESSION_DIR/latest" mkdir -p "$RK_LOG_DIR" ln -rsf "$RK_SESSION_DIR" "$RK_LOG_BASE_DIR" ln -rsf "$RK_LOG_DIR" "$RK_SESSION_DIR/latest" message "Log saved at $RK_LOG_DIR" fi # Drop old logs cd "$RK_LOG_BASE_DIR" rm -rf $(ls -t | sed '1,10d') cd "$RK_SDK_DIR" # Save initial envionments if [ "$INITIAL_SESSION" ]; then rm -f "$RK_INITIAL_ENV" cp "$INITIAL_ENV" "$RK_INITIAL_ENV" ln -rsf "$RK_INITIAL_ENV" "$RK_OUTDIR/" fi rm -f "$INITIAL_ENV" # Init stage (preparing SDK configs, etc.) run_build_hooks init $OPTIONS rm -f "$RK_OUTDIR/.tmpconfig*" # No need to go further CMDS="$RK_PRE_BUILD_CMDS $RK_BUILD_CMDS $RK_POST_BUILD_CMDS \ cleanall clean-.* post-rootfs" option_check "$CMDS" $OPTIONS || return 0 # Force exporting config environments set -a # Load config environments source "$RK_CONFIG" cp "$RK_CONFIG" "$RK_LOG_DIR" export RK_KERNEL_VERSION="$(kernel_version)" if [ -z "$INITIAL_SESSION" ]; then # Inherit session environments sed -n 's/^\(RK_.*=\)\(.*\)/\1"\2"/p' "$RK_FINAL_ENV" > \ "$INITIAL_ENV" source "$INITIAL_ENV" rm -f "$INITIAL_ENV" else # Detect and save custom environments # Find custom environments rm -f "$RK_CUSTOM_ENV" for cfg in $(grep "^RK_" "$RK_INITIAL_ENV" || true); do env | grep -q "^${cfg//\"/}$" || \ echo "$cfg" >> "$RK_CUSTOM_ENV" done # Allow custom environments overriding if [ -e "$RK_CUSTOM_ENV" ]; then ln -rsf "$RK_CUSTOM_ENV" "$RK_OUTDIR/" warning "WARN: Found custom environments:" cat "$RK_CUSTOM_ENV" warning "Assuming that is expected, please clear them if otherwise." read -t 10 -p "Press enter to continue." source "$RK_CUSTOM_ENV" if grep -q "^RK_KERNEL_VERSION=" "$RK_CUSTOM_ENV"; then warning "Custom RK_KERNEL_VERSION ignored!" fi if grep -q "^RK_ROOTFS_SYSTEM=" "$RK_CUSTOM_ENV"; then warning "Custom RK_ROOTFS_SYSTEM ignored!" load_config RK_ROOTFS_SYSTEM fi fi fi # Parse partition table source "$RK_PARTITION_HELPER" rk_partition_init set +a # The real kernel version: 4.4/4.19/5.10/6.1, etc. export RK_KERNEL_VERSION_RAW=$(kernel_version_raw) export RK_KERNEL_VERSION="$(kernel_version)" # Handle special commands case "$OPTIONS" in cleanall) run_build_hooks clean rm -rf "$RK_OUTDIR" "$RK_SDK_DIR/rockdev" finish_build cleanall exit 0 ;; clean-*) MODULE="$(echo ${OPTIONS#clean-})" if [ -x "$RK_CHIP_SCRIPTS_DIR/mk-$MODULE.sh" ]; then "$RK_CHIP_SCRIPTS_DIR/mk-$MODULE.sh" clean else "$RK_SCRIPTS_DIR/mk-$MODULE.sh" clean fi finish_build clean - $MODULE exit 0 ;; post-rootfs) shift touch "$RK_LOG_DIR/.stamp_post_start" run_post_hooks "$@" TARGET_DIR="$1" source "$RK_POST_HELPER" POST_DIR="$RK_OUTDIR/$POST_OS" mkdir -p "$POST_DIR" ln -rsf "$TARGET_DIR" "$POST_DIR/target" finish_build post-rootfs notice "Files changed in post-rootfs stage:" cd "$TARGET_DIR" find . \( -type f -o -type l \) \ -cnewer "$RK_LOG_DIR/.stamp_post_start" | \ tee "$POST_DIR/.files_post.txt" exit 0 ;; esac # Save final environments rm -f "$RK_FINAL_ENV" env > "$RK_FINAL_ENV" ln -rsf "$RK_FINAL_ENV" "$RK_OUTDIR/" # Log configs message "\n==========================================" message " Final configs" message "==========================================" env | grep -E "^RK_.*=.+" | grep -vE "PARTITION_[0-9]" | \ grep -vE "=\"\"$|_DEFAULT=y|^RK_DEFAULT_TARGET|CMDS=" | \ grep -vE "^RK_CONFIG|_BASE_CFG=|_LINK=|DIR=|_ENV=|_NAME=|_DTB=" | \ grep -vE "_HELPER=|_SUPPORTS=|_ARM64=|_ARM=|_HOST=" | \ grep -vE "^RK_ROOTFS_SYSTEM_|^RK_YOCTO_DISPLAY_PLATFORM_" | sort echo # Pre-build stage (submodule configuring, etc.) run_build_hooks pre-build $OPTIONS # Build stage (building, etc.) run_build_hooks build $OPTIONS # Post-build stage (firmware packing, etc.) run_build_hooks post-build $OPTIONS } if [ "$0" != "$BASH_SOURCE" ]; then # Sourced, executing it directly "$BASH_SOURCE" ${@:-shell} elif [ "$0" == "$BASH_SOURCE" ]; then # Executed directly main "${@%%:}" fi
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