diff --git a/README.md b/README.md index 9f9a561d..d60f5144 100644 --- a/README.md +++ b/README.md @@ -145,7 +145,7 @@ Visit the [man page](https://hasindu2008.github.io/f5c/docs/commands) for all th Follow the same steps as in [Nanopolish tutorial](https://nanopolish.readthedocs.io/en/latest/quickstart_call_methylation.html) while replacing `nanopolish` with `f5c`. If you only want to perform a quick test of f5c : ```sh #download and extract the dataset including sorted alignments -wget -O f5c_na12878_test.tgz "https://f5c.page.link/f5c_na12878_test" +wget -O f5c_na12878_test.tgz "https://f5c.bioinf.science/f5c_na12878_test" tar xf f5c_na12878_test.tgz ###### Using S/BLOW5 as input (recommended) ###### diff --git a/scripts/install-vbz.sh b/scripts/install-vbz.sh index cf3dc672..7ae173a3 100755 --- a/scripts/install-vbz.sh +++ b/scripts/install-vbz.sh @@ -21,7 +21,7 @@ print() { echo -e "${GREEN}$1${NC}" >&2 } -MANUAL_LINK="https://f5c.page.link/troubleshoot" +MANUAL_LINK="https://f5c.bioinf.science/troubleshoot" uname -o || die "Could not determine the O/S. See ${MANUAL_LINK}" uname -m || die "Could not determine the architecture. See ${MANUAL_LINK}" diff --git a/scripts/test.sh b/scripts/test.sh index 4812e267..a35c848c 100755 --- a/scripts/test.sh +++ b/scripts/test.sh @@ -21,8 +21,8 @@ else fi # execution mode (valgrind/gdb/cpu/cuda/echo) mode= -testset_url="https://f5c.page.link/f5c_ecoli_2kb_region_test" -fallback_url="https://f5c.page.link/f5c_ecoli_2kb_region_test_fallback" +testset_url="https://f5c.bioinf.science/f5c_ecoli_2kb_region_test" +fallback_url="https://f5c.bioinf.science/f5c_ecoli_2kb_region_test_fallback" # download test set given url # @@ -131,17 +131,17 @@ do bamfile=${testdir}/reads.sorted.bam ref=${testdir}/humangenome.fa reads=${testdir}/reads.fastq - testset_url="https://f5c.page.link/f5c_na12878_test" - fallback_url="https://f5c.page.link/f5c_na12878_test_fallback";; + testset_url="https://f5c.bioinf.science/f5c_na12878_test" + fallback_url="https://f5c.bioinf.science/f5c_na12878_test_fallback";; f) testdir=test/hg2_lsk114_reads_1000 reads=${testdir}/PGXX22394_reads_1000_6.4.2_sup.fastq slow5=${testdir}/PGXX22394_reads_1000.blow5 ref=test/chr22_meth_example/humangenome.fa bamfile=${testdir}/PGXX22394_reads_1000_6.4.2_sup.bam - testset_url="https://f5c.page.link/hg2_lsk114_reads_1000";; + testset_url="https://f5c.bioinf.science/hg2_lsk114_reads_1000";; K) batchsize="$OPTARG";; B) max_bases="$OPTARG";; - d) download_test_set "https://f5c.page.link/f5c_na12878_test" "https://f5c.page.link/f5c_na12878_test_fallback" + d) download_test_set "https://f5c.bioinf.science/f5c_na12878_test" "https://f5c.bioinf.science/f5c_na12878_test_fallback" exit 0;; h) help_msg exit 0;; diff --git a/src/error.h b/src/error.h index f58daa5c..3da3d95b 100644 --- a/src/error.h +++ b/src/error.h @@ -50,7 +50,7 @@ static inline void malloc_chk(void* ret, const char* func, const char* file, "[%s::ERROR]\033[1;31m Failed to allocate memory : " "%s.\033[0m\n[%s::DEBUG]\033[1;35m Error occured at %s:%d. Try with a small batchsize (-K and/or -B options)," "fewer threads (-t) or skip ultra-long reads (--skip-ultra) to reduce the peak memory." - "See https://f5c.page.link/troubleshoot for details.\033[0m\n\n", + "See https://f5c.bioinf.science/troubleshoot for details.\033[0m\n\n", func, strerror(errno), func, file, line); exit(EXIT_FAILURE); } diff --git a/src/fast5lite.h b/src/fast5lite.h index 884dd408..8038bfa4 100644 --- a/src/fast5lite.h +++ b/src/fast5lite.h @@ -294,7 +294,7 @@ static inline int32_t fast5_read_multi_fast5(fast5_file_t fh, signal_t* sig, std if (status < 0) { free(sig->rawptr); if(fast5_is_vbz_compressed(fh, read_id) == 1) { - ERROR("%s","The fast5 file is compressed with VBZ but the required plugin is not loaded. See https://f5c.page.link/troubleshoot for instructions.\n"); + ERROR("%s","The fast5 file is compressed with VBZ but the required plugin is not loaded. See https://f5c.bioinf.science/troubleshoot for instructions.\n"); } WARNING("Failed to read raw data from dataset %s.", signal_path); H5Sclose(space); diff --git a/src/freq.c b/src/freq.c index 20d228e8..e2987fc2 100644 --- a/src/freq.c +++ b/src/freq.c @@ -34,7 +34,7 @@ static const char usage[] = "Usage: %s [OPTIONS] -i methcalls.tsv\n" " -s split groups\n" " -h help\n" " --version print version\n" - "\nSee the manual page for details (`man ./docs/f5c.1' or https://f5c.page.link/man).\n" + "\nSee the manual page for details (`man ./docs/f5c.1' or https://f5c.bioinf.science/man).\n" ; struct site_stats { diff --git a/src/freq_merge.c b/src/freq_merge.c index 9ce6703f..675d52fc 100644 --- a/src/freq_merge.c +++ b/src/freq_merge.c @@ -136,7 +136,7 @@ static const char *MAP_REDUCE_USAGE_MESSAGE = " -o FILE output file. Write to stdout if not specified\n" " -h help\n" " --version print version\n" - "\nSee the manual page for details (`man ./docs/f5c.1' or https://f5c.page.link/man)." + "\nSee the manual page for details (`man ./docs/f5c.1' or https://f5c.bioinf.science/man)." "\n\n" ; diff --git a/src/index.c b/src/index.c index f8782872..7a9362fe 100644 --- a/src/index.c +++ b/src/index.c @@ -76,7 +76,7 @@ static const char *INDEX_USAGE_MESSAGE = " --skip-slow5-idx do not build the .idx for the slow5 file (useful when a slow5 index is already available)\n" " --verbose INT verbosity level\n" " --version print version\n" -"\nSee the manual page for details (`man ./docs/f5c.1' or https://f5c.page.link/man)." +"\nSee the manual page for details (`man ./docs/f5c.1' or https://f5c.bioinf.science/man)." "\n\n" ; diff --git a/src/main.c b/src/main.c index cbe903df..88bd064f 100644 --- a/src/main.c +++ b/src/main.c @@ -56,7 +56,7 @@ int print_usage(FILE *fp_help){ fprintf(fp_help," eventalign Align nanopore events to reference k-mers (optimised nanopolish eventalign)\n"); fprintf(fp_help," freq-merge Merge calculated methylation frequency tsv files\n"); fprintf(fp_help," resquiggle Align raw signals to basecalled reads\n"); - fprintf(fp_help,"\nSee the manual page for details (`man ./docs/f5c.1' or https://f5c.page.link/man).\n"); + fprintf(fp_help,"\nSee the manual page for details (`man ./docs/f5c.1' or https://f5c.bioinf.science/man).\n"); if(fp_help==stderr){ exit(EXIT_FAILURE); } diff --git a/src/meth_main.c b/src/meth_main.c index a42560cb..4d9e0e58 100644 --- a/src/meth_main.c +++ b/src/meth_main.c @@ -483,7 +483,7 @@ int meth_main(int argc, char* argv[], int8_t mode) { fprintf(fp_help," -h help\n"); fprintf(fp_help," -o FILE output to file [stdout]\n"); fprintf(fp_help," -x STR parameter profile to be used for better performance (always applied before other options)\n"); //Added option in help - fprintf(fp_help," e.g., laptop, desktop, hpc; see https://f5c.page.link/profiles for the full list\n"); + fprintf(fp_help," e.g., laptop, desktop, hpc; see https://f5c.bioinf.science/profiles for the full list\n"); fprintf(fp_help," --iop INT number of I/O processes to read fast5 files [%d]\n",opt.num_iop); fprintf(fp_help," --pore STR set the pore chemistry (r9, r10 or rna004) [r9]\n"); fprintf(fp_help," --slow5 FILE read from a slow5 file\n"); @@ -536,7 +536,7 @@ int meth_main(int argc, char* argv[], int8_t mode) { fprintf(fp_help," --profile-cpu=yes|no process section by section (used for profiling on CPU)\n"); fprintf(fp_help," --write-dump=yes|no write the fast5 dump to a file or not\n"); fprintf(fp_help," --read-dump=yes|no read from a fast5 dump file or not\n"); - fprintf(fp_help,"\nSee the manual page for details (`man ./docs/f5c.1' or https://f5c.page.link/man).\n"); + fprintf(fp_help,"\nSee the manual page for details (`man ./docs/f5c.1' or https://f5c.bioinf.science/man).\n"); if(fp_help == stdout){ exit(EXIT_SUCCESS); } diff --git a/src/resquiggle.c b/src/resquiggle.c index 3491f17b..4cb1cbb4 100644 --- a/src/resquiggle.c +++ b/src/resquiggle.c @@ -42,7 +42,7 @@ static void print_help_msg(FILE *fp_help, opt_t opt){ fprintf(fp_help," -h help\n"); fprintf(fp_help," -o FILE output to file [stdout]\n"); fprintf(fp_help," -x STR parameter profile to be used for better performance (always applied before other options)\n"); //Added option in help - fprintf(fp_help," e.g., laptop, desktop, hpc; see https://f5c.page.link/profiles for the full list\n"); + fprintf(fp_help," e.g., laptop, desktop, hpc; see https://f5c.bioinf.science/profiles for the full list\n"); fprintf(fp_help," -c print in paf format\n"); fprintf(fp_help," --verbose INT verbosity level [%d]\n",opt.verbosity); fprintf(fp_help," --version print version\n");