mosdepth
mosdepth copied to clipboard
brentp
Mac OSX
Is there a way to install this tool on a mac osx?
brew install brewsci/bio/mosdepth ==> Installing mosdepth from brewsci/bio mosdepth: Linux is required. Error: An unsatisfied requirement failed this build.
conda install mosdepth Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- mosdepth
Current channels:
- https://repo.anaconda.com/pkgs/main/osx-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/osx-64
- https://repo.anaconda.com/pkgs/r/noarch
To search for alternate channels that may provide the conda package you're looking for, navigate to
https://anaconda.org
Both conda and brew failed.
conda install -c bioconda mosdepth Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- mosdepth
Current channels:
- https://conda.anaconda.org/bioconda/osx-64
- https://conda.anaconda.org/bioconda/noarch
- https://repo.anaconda.com/pkgs/main/osx-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/osx-64
- https://repo.anaconda.com/pkgs/r/noarch
To search for alternate channels that may provide the conda package you're looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
hmm. looks like the recipe skips OSX: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/mosdepth/meta.yaml not sure why. you can build yourself by installing nim (just get choosenim and then nimble install -y mosdepth)
nimble install -y mosdepth --verbose Reading official package list Prompt: mosdepth not found in any local packages.json, check internet for updated packages? -> [forced yes] Downloading Official package list Trying https://github.com/nim-lang/packages/raw/master/packages.json Success Package list downloaded. Reading official package list Error: Package not found.
ah right. please try this:
git clone https://github.com/brentp/mosdepth
cd mosdepth
nimble install -y
nim c -d:danger -d:release mosdepth.nim
./mosdepth -h
Verifying dependencies for [email protected] Info: Dependency on hts@>= 0.3.1 already satisfied Verifying dependencies for [email protected] Info: Dependency on docopt@>= 0.6.8 already satisfied Verifying dependencies for [email protected] Info: Dependency on regex@>= 0.7.4 already satisfied Verifying dependencies for [email protected] Info: Dependency on unicodedb@>= 0.7.2 already satisfied Verifying dependencies for [email protected] Info: Dependency on unicodeplus@>= 0.5.0 already satisfied Verifying dependencies for [email protected] Info: Dependency on unicodedb@>= 0.7 already satisfied Verifying dependencies for [email protected] Installing [email protected] Building mosdepth/mosdepth using c backend Tip: 17 messages have been suppressed, use --verbose to show them. Error: Build failed for package: mosdepth ... Details: ... Execution failed with exit code 1 ... Command: "/usr/local/Cellar/nim/1.0.4/nim/bin/nim" c --noNimblePath -d:NimblePkgVersion=0.2.8 -d:release --path:"/Users/ksarathbabu/.nimble/pkgs/hts-0.3.2" --path:"/Users/ksarathbabu/.nimble/pkgs/docopt-0.6.8" --path:"/Users/ksarathbabu/.nimble/pkgs/regex-0.13.0" --path:"/Users/ksarathbabu/.nimble/pkgs/unicodedb-0.7.2" --path:"/Users/ksarathbabu/.nimble/pkgs/unicodeplus-0.5.1" --path:"/Users/ksarathbabu/.nimble/pkgs/unicodedb-0.7.2" -o:"/Users/ksarathbabu/Desktop/Tools/mosdepth/mosdepth" "/Users/ksarathbabu/Desktop/Tools/mosdepth/mosdepth.nim" ... Output: Hint: used config file '/usr/local/Cellar/nim/1.0.4/nim/config/nim.cfg' [Conf] ... Hint: used config file '/Users/ksarathbabu/Desktop/Tools/mosdepth/nim.cfg' [Conf] ... Hint: system [Processing] ... Hint: widestrs [Processing] ... Hint: io [Processing] ... Hint: mosdepth [Processing] ... Hint: hts [Processing] ... Hint: utils [Processing] ... Hint: hts_concat [Processing] ... Hint: bam [Processing] ... Hint: strformat [Processing] ... Hint: macros [Processing] ... Hint: parseutils [Processing] ... Hint: unicode [Processing] ... Hint: strutils [Processing] ... Hint: math [Processing] ... Hint: bitops [Processing] ... Hint: algorithm [Processing] ... Hint: simpleoption [Processing] ... Hint: typetraits [Processing] ... Hint: vcf [Processing] ... Hint: sequtils [Processing] ... Hint: fai [Processing] ... Hint: bgzf [Processing] ... Hint: bgzi [Processing] ... Hint: csi [Processing] ... Hint: stats [Processing] ... Hint: tables [Processing] ... Hint: hashes [Processing] ... Hint: os [Processing] ... Hint: pathnorm [Processing] ... Hint: osseps [Processing] ... Hint: posix [Processing] ... Hint: times [Processing] ... Hint: options [Processing] ... Hint: docopt [Processing] ... Hint: regex [Processing] ... Hint: sets [Processing] ... Hint: properties [Processing] ... Hint: properties_data [Processing] ... Hint: types [Processing] ... Hint: types_data [Processing] ... Hint: unicodeplus [Processing] ... Hint: util [Processing] ... Hint: depthstat [Processing] ... /Users/ksarathbabu/Desktop/Tools/mosdepth/mosdepth.nim(9, 8) Warning: imported and not used: 'times' [UnusedImport] ... CC: ../../../.nimble/pkgs/hts-0.3.2/hts/private/hts_concat.nim ... CC: ../../../.nimble/pkgs/hts-0.3.2/hts/bam.nim ... CC: ../../../.nimble/pkgs/hts-0.3.2/hts/vcf.nim ... CC: ../../../.nimble/pkgs/hts-0.3.2/hts/bgzf.nim ... CC: ../../../.nimble/pkgs/hts-0.3.2/hts/csi.nim ... CC: ../../../.nimble/pkgs/hts-0.3.2/hts/bgzf/bgzi.nim ... CC: ../../../.nimble/pkgs/hts-0.3.2/hts.nim ... CC: ../../../.nimble/pkgs/unicodeplus-0.5.1/unicodeplus.nim ... CC: ../../../.nimble/pkgs/regex-0.13.0/regex.nim ... CC: ../../../.nimble/pkgs/docopt-0.6.8/docopt/util.nim ... CC: ../../../.nimble/pkgs/docopt-0.6.8/docopt.nim ... Hint: [Link] ... ld: warning: ignoring file /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libm.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libm.tbd ... ld: warning: ignoring file /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libdl.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libdl.tbd ... ld: warning: ignoring file /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd ... Undefined symbols for architecture x86_64: ... "__NSGetEnviron", referenced from: ... _getEnvVarsC__580467zYn32AEdYj9cD4LLA in stdlib_os.nim.c.o ... "___bzero", referenced from: ... _llAlloc__ovw3NMWXeZ0Qi9cGYq1E2Tg in stdlib_system.nim.c.o ... _addHeapLink__LIRFHBfc9aX3C5dmMmLnpwA in stdlib_system.nim.c.o ... _alloc0__UxtcZ3QOXKsB7mMchxUf9cg in stdlib_system.nim.c.o ... _alloc0__WrVG9abV9chlTLqkiXYLKwUg in stdlib_system.nim.c.o ... _init__wKM37ZoL6WtPOU9bn6Ug18A in stdlib_system.nim.c.o ... _init__Y9c9cQhDWRSgYkHfKWcqFlsQ in stdlib_system.nim.c.o ... _cellSetEnlarge__9bhPFIGFYIneoHljx8OXvqA in stdlib_system.nim.c.o ... ... ... "___error", referenced from: ... _checkErr__fU6ZlJAtQ9bre04EDZLdGsA in stdlib_io.nim.c.o ... _open__9aPjGS9a9a5nGpS0viBU29aJXQ in @m..@s..@[email protected]@[email protected]@[email protected] ... "___memcpy_chk", referenced from: ... _raiseExceptionAux__na8C8pUZ9cLQWVwk35l5vfw in stdlib_system.nim.c.o ... "___sprintf_chk", referenced from: ... _nsuformatBiggestFloat in stdlib_strutils.nim.c.o ... "___stack_chk_fail", referenced from: ... _markStackAndRegisters__U6T7JWtDLrWhtmhXSoy9a6g in stdlib_system.nim.c.o ... _raiseExceptionAux__na8C8pUZ9cLQWVwk35l5vfw in stdlib_system.nim.c.o ... _nsuReplaceStr in stdlib_strutils.nim.c.o ... _nsuFindStr in stdlib_strutils.nim.c.o ... _nsuformatBiggestFloat in stdlib_strutils.nim.c.o ... _dollar___SnhqCM7DrEz2CWkWdVIcXg in @m..@s..@[email protected]@[email protected]@[email protected] ... _idx_set_meta__yvSvcCZ3AjP312uJak0ypA in @m..@s..@[email protected]@[email protected]@[email protected] ... ... ... "___stack_chk_guard", referenced from: ... _markStackAndRegisters__U6T7JWtDLrWhtmhXSoy9a6g in stdlib_system.nim.c.o ... _raiseExceptionAux__na8C8pUZ9cLQWVwk35l5vfw in stdlib_system.nim.c.o ... _nsuReplaceStr in stdlib_strutils.nim.c.o ... _nsuFindStr in stdlib_strutils.nim.c.o ... _nsuformatBiggestFloat in stdlib_strutils.nim.c.o ... _dollar___SnhqCM7DrEz2CWkWdVIcXg in @m..@s..@[email protected]@[email protected]@[email protected] ... _idx_set_meta__yvSvcCZ3AjP312uJak0ypA in @m..@s..@[email protected]@[email protected]@[email protected] ... ... ... "___stderrp", referenced from: ... _raiseOutOfMem__mMRdr4sgmnykA9aWeM9aDZlw in stdlib_system.nim.c.o ... _writeToStdErr__a2kDfqdSc1eYf0ZCWOGinQ in stdlib_system.nim.c.o ... _showErrorMessage__zsORN9crdKxsL9cHrQcdHSMw in stdlib_system.nim.c.o ... _nimRegisterThreadLocalMarker in stdlib_system.nim.c.o ... _nimRegisterGlobalMarker in stdlib_system.nim.c.o ... _nimLoadLibraryError in stdlib_system.nim.c.o ... _procAddrError in stdlib_system.nim.c.o ... ... ... "___stdoutp", referenced from: ... _echoBinSafe in stdlib_io.nim.c.o ... "__longjmp", referenced from: ... _raiseExceptionAux__na8C8pUZ9cLQWVwk35l5vfw in stdlib_system.nim.c.o ... "__setjmp", referenced from: ... _markStackAndRegisters__U6T7JWtDLrWhtmhXSoy9a6g in stdlib_system.nim.c.o ... _match__mElywvmHW9csPAv8cNiHClg in @m..@s..@[email protected]@[email protected]@sdocopt.nim.c.o ... _docopt__1Ouo477jH9cQS4owbam42Ww in @m..@s..@[email protected]@[email protected]@sdocopt.nim.c.o ... _get_quantize_args__9cbDihDBsDMr1ZwNMjGgWfw in @mmosdepth.nim.c.o ... _NimMainModule in @mmosdepth.nim.c.o ... "_clearerr", referenced from: ... _checkErr__fU6ZlJAtQ9bre04EDZLdGsA in stdlib_io.nim.c.o ... "_dlopen", referenced from: ... _nimLoadLibrary in stdlib_system.nim.c.o ... "_dlsym", referenced from: ... _nimGetProcAddr in stdlib_system.nim.c.o ... "_exit", referenced from: ... _raiseOutOfMem__mMRdr4sgmnykA9aWeM9aDZlw in stdlib_system.nim.c.o ... _raiseExceptionAux__na8C8pUZ9cLQWVwk35l5vfw in stdlib_system.nim.c.o ... _nimRegisterThreadLocalMarker in stdlib_system.nim.c.o ... _signalHandler in stdlib_system.nim.c.o ... _nimRegisterGlobalMarker in stdlib_system.nim.c.o ... _nimLoadLibraryError in stdlib_system.nim.c.o ... _procAddrError in stdlib_system.nim.c.o ... ... ... "_fclose", referenced from: ... _close__fU6ZlJAtQ9bre04EDZLdGsA_2 in stdlib_io.nim.c.o ... _open__gq12VLhVO0NBzUTnGgz4nw in stdlib_io.nim.c.o ... "_ferror", referenced from: ... _checkErr__fU6ZlJAtQ9bre04EDZLdGsA in stdlib_io.nim.c.o ... "_fflush", referenced from: ... _echoBinSafe in stdlib_io.nim.c.o ... "_fileno", referenced from: ... _getFileHandle__hOwLbM7eXaZgEJrHWLeiNg in stdlib_io.nim.c.o ... _open__gq12VLhVO0NBzUTnGgz4nw in stdlib_io.nim.c.o ... "_flockfile", referenced from: ... _echoBinSafe in stdlib_io.nim.c.o ... "_fopen", referenced from: ... _open__gq12VLhVO0NBzUTnGgz4nw in stdlib_io.nim.c.o ... "_free", referenced from: ... _bed_to_table__kYJ7WK9a20hsAj39cJfRlU9cA in @mmosdepth.nim.c.o ... (maybe you meant: _freeBigChunk__IPvsryqksLyNxxag3IQr2g, _freeCyclicCell__SOJE9bROCOc8iabVsKM64Sg_2 , _freeHugeChunk__IPvsryqksLyNxxag3IQr2g_2 ) ... "_fstat$INODE64", referenced from: ... _open__gq12VLhVO0NBzUTnGgz4nw in stdlib_io.nim.c.o ... "_funlockfile", referenced from: ... _echoBinSafe in stdlib_io.nim.c.o ... "_fwrite", referenced from: ... _echoBinSafe in stdlib_io.nim.c.o ... _writeBuffer__Y9atVWUcVyKHG9aBP4D0P9czA in stdlib_io.nim.c.o ... _write__PArlm09bKklm2BLsCg6YtaA in stdlib_io.nim.c.o ... _rawWrite in stdlib_system.nim.c.o ... _writeToStdErr__a2kDfqdSc1eYf0ZCWOGinQ in stdlib_system.nim.c.o ... _showErrorMessage__zsORN9crdKxsL9cHrQcdHSMw in stdlib_system.nim.c.o ... _nimLoadLibraryError in stdlib_system.nim.c.o ... ... ... "_getenv", referenced from: ... _getEnv__hhED57tMl0Iaa5bOg9cJaig in stdlib_os.nim.c.o ... "_memchr", referenced from: ... _nsuFindChar in stdlib_strutils.nim.c.o ... "_memcmp", referenced from: ... _X5BX5Deq___78Q4dxBweRhgjG7B9cI9cApw in stdlib_tables.nim.c.o ... _rawGet__mNTOeh9adJNQYWgUiiILTSgtables in stdlib_tables.nim.c.o ... _hasKeyOrPut__3KDoYrjxY3k3NFOBdG4HeA in stdlib_tables.nim.c.o ... _rawGet__QcwT358CAl4HKrtxytUebAtables in stdlib_tables.nim.c.o ... _rawGet__fuQlYMkPYoYe9bnsumTP8vQtables in stdlib_tables.nim.c.o ... _X5BX5Deq___rNiqEa3vCNvEGATZR9cTNEg in stdlib_tables.nim.c.o ... _is_upper__rhwqFXsVV4qtCGtLPYyqBQ in @m..@s..@[email protected]@[email protected]@[email protected] ... ... ... "_memcpy", referenced from: ... _appendString in stdlib_io.nim.c.o ... _addZCT__Y66tOYFjgwJ0k4aLz4bc0Q in stdlib_system.nim.c.o ... _doOperation__sl6eqhLncFedgwzv6TlMVw in stdlib_system.nim.c.o ... _markStackAndRegisters__U6T7JWtDLrWhtmhXSoy9a6g in stdlib_system.nim.c.o ... _sweep__XHio9cMpnLoH7GyCj1Z9besg_5 in stdlib_system.nim.c.o ... _rawNewObj__ehkAaLROrd0Hc9aLROWt1nQ in stdlib_system.nim.c.o ... _copyStringRC1 in stdlib_system.nim.c.o ... ... ... "_mmap", referenced from: ... _llAlloc__ovw3NMWXeZ0Qi9cGYq1E2Tg in stdlib_system.nim.c.o ... _addHeapLink__LIRFHBfc9aX3C5dmMmLnpwA in stdlib_system.nim.c.o ... _requestOsChunks__stlXHMKRKFIGOvq8t4ynRQ_2 in stdlib_system.nim.c.o ... _intSetPut__Cw86Sj6YgVACdT20AkWjcA in stdlib_system.nim.c.o ... _getHugeChunk__stlXHMKRKFIGOvq8t4ynRQ_3 in stdlib_system.nim.c.o ... _allocAvlNode__Du8pyfSfDLyN9aoS2IcBsHg in stdlib_system.nim.c.o ... _rawAlloc__mE4QEVyMvGRVliDWDngZCQ in stdlib_system.nim.c.o ... ... ... "_munmap", referenced from: ... _freeHugeChunk__IPvsryqksLyNxxag3IQr2g_2 in stdlib_system.nim.c.o ... _rawDealloc__K7uQ6aTKvW6OnOV8EMoNNQ in stdlib_system.nim.c.o ... "_setvbuf", referenced from: ... _open__gq12VLhVO0NBzUTnGgz4nw in stdlib_io.nim.c.o ... "_signal", referenced from: ... _registerSignalHandler__amVlU9ajqZ06ujoesRBHcDg_2 in stdlib_system.nim.c.o ... _systemInit000 in stdlib_system.nim.c.o ... (maybe you meant: _signalHandler) ... "_stat$INODE64", referenced from: ... _nosexistsFile in stdlib_os.nim.c.o ... "_strcmp", referenced from: ... _coverage__XiKKDqFArqrfTLMadktcEg in @mmosdepth.nim.c.o ... "_strerror", referenced from: ... _checkErr__fU6ZlJAtQ9bre04EDZLdGsA in stdlib_io.nim.c.o ... _open__9aPjGS9a9a5nGpS0viBU29aJXQ in @m..@s..@[email protected]@[email protected]@[email protected] ... "_strlen", referenced from: ... _rawWrite in stdlib_system.nim.c.o ... _cstrToNimstr in stdlib_system.nim.c.o ... _writeToStdErr__a2kDfqdSc1eYf0ZCWOGinQ in stdlib_system.nim.c.o ... _showErrorMessage__zsORN9crdKxsL9cHrQcdHSMw in stdlib_system.nim.c.o ... _raiseExceptionAux__na8C8pUZ9cLQWVwk35l5vfw in stdlib_system.nim.c.o ... "_tzset", referenced from: ... _stdlib_timesInit000 in stdlib_times.nim.c.o ... ld: symbol(s) not found for architecture x86_64 ... clang-4.0: error: linker command failed with exit code 1 (use -v to see invocation) ... Error: execution of an external program failed: 'clang -o /Users/ksarathbabu/Desktop/Tools/mosdepth/mosdepth /Users/ksarathbabu/.cache/nim/mosdepth_r/stdlib_assertions.nim.c.o /Users/ksarathbabu/.cache/nim/mosdepth_r/stdlib_io.nim.c.o /Users/ksarathbabu/.cache/nim/mosdepth_r/stdlib_system.nim.c.o /Users/ksarathbabu/.cache/nim/mosdepth_r/@m..@s..@[email protected]@[email protected]@shts@sprivate@shts_concat.nim.c.o /Users/ksarathbabu/.cache/nim/mosdepth_r/stdlib_parseutils.nim.c.o /Users/ksarathbabu/.cache/nim/mosdepth_r/stdlib_unicode.nim.c.o /Users/ksarathbabu/.cache/nim/mosdepth_r/stdlib_math.nim.c.o /Users/ksarathbabu/.cache/nim/mosdepth_r/stdlib_algorithm.nim.c.o /Users/ksarathbabu/.cache/nim/mosdepth_r/stdlib_strutils.nim.c.o /Users/ksarathbabu/.cache/nim/mosdepth_r/stdlib_strformat.nim.c.o /Users/ksarathbabu/.cache/nim/mosdepth_r/@m..@s..@[email protected]@[email protected]@[email protected] /Users/ksarathbabu/.cache/nim/mosdepth_r/stdlib_sequtils.nim.c.o /Users/ksarathbabu/.cache/nim/mosdepth_r/@m..@s..@[email protected]@[email protected]@[email protected] /Users/ksarathbabu/.cache/nim/mosdepth_r/@m..@s..@[email protected]@[email protected]@[email protected] /Users/ksarathbabu/.cache/nim/mosdepth_r/@m..@s..@[email protected]@[email protected]@[email protected] /Users/ksarathbabu/.cache/nim/mosdepth_r/@m..@s..@[email protected]@[email protected]@shts@[email protected] /Users/ksarathbabu/.cache/nim/mosdepth_r/@m..@s..@[email protected]@[email protected]@shts.nim.c.o /Users/ksarathbabu/.cache/nim/mosdepth_r/stdlib_hashes.nim.c.o /Users/ksarathbabu/.cache/nim/mosdepth_r/stdlib_tables.nim.c.o /Users/ksarathbabu/.cache/nim/mosdepth_r/stdlib_posix.nim.c.o /Users/ksarathbabu/.cache/nim/mosdepth_r/stdlib_times.nim.c.o /Users/ksarathbabu/.cache/nim/mosdepth_r/stdlib_os.nim.c.o /Users/ksarathbabu/.cache/nim/mosdepth_r/stdlib_sets.nim.c.o /Users/ksarathbabu/.cache/nim/mosdepth_r/@m..@s..@[email protected]@[email protected]@sunicodedb@sproperties_data.nim.c.o /Users/ksarathbabu/.cache/nim/mosdepth_r/@m..@s..@[email protected]@[email protected]@[email protected] /Users/ksarathbabu/.cache/nim/mosdepth_r/@m..@s..@[email protected]@[email protected]@sunicodedb@stypes_data.nim.c.o /Users/ksarathbabu/.cache/nim/mosdepth_r/@m..@s..@[email protected]@[email protected]@[email protected] /Users/ksarathbabu/.cache/nim/mosdepth_r/@m..@s..@[email protected]@[email protected]@sunicodeplus.nim.c.o /Users/ksarathbabu/.cache/nim/mosdepth_r/@m..@s..@[email protected]@[email protected]@sregex.nim.c.o /Users/ksarathbabu/.cache/nim/mosdepth_r/@m..@s..@[email protected]@[email protected]@[email protected] /Users/ksarathbabu/.cache/nim/mosdepth_r/@m..@s..@[email protected]@[email protected]@sdocopt.nim.c.o /Users/ksarathbabu/.cache/nim/mosdepth_r/@mdepthstat.nim.c.o /Users/ksarathbabu/.cache/nim/mosdepth_r/@mmosdepth.nim.c.o -lm -ldl'
I will try to look into this and getting the OSX bioconda build working (I don't use OSX), thanks for reporting the output. I think in short term your best bet is to use docker or run mosdepth on linux.
Thanks for looking into this, just adding another voice to the request, since it looks like such an awesome tool.
If anyone cares: For me (macOS 10.14.6) the following steps allowed to build mosdepth from scratch:
- get Nim via https://github.com/dom96/choosenim and follow instructions. Put into PATH (as instructed during the installation).
- get htslib, e.g. via conda and then put the lib folder into your LD_LIBRARY_PATH, e.g.:
(export LD_LIBRARY_PATH=~/path/to/conda/lib). It is the folder that contains
htslib.dylibwhich has to be in that path. Must be htslib >= 1.10 get hts-nim (https://github.com/brentp/hts-nim) and build withEdit: I did step 3 manually, but actually just realized that skipping it and running 4) directly will automatically pull hts-nim if step 2 was done properly andnimble install -yhtslib.dylibis available via theLD_LIBRARY_PATH.- get mosdepth source package and install via
nimble install -y. After this I was able to successfully run mosdepth.
A bit cleaner version: https://www.biostars.org/p/437365/
No, this always returns:
$ brew install brewsci/bio/mosdepth
==> Tapping brewsci/bio
Cloning into '/usr/local/Homebrew/Library/Taps/brewsci/homebrew-bio'...
remote: Enumerating objects: 94, done.
remote: Counting objects: 100% (94/94), done.
remote: Compressing objects: 100% (68/68), done.
remote: Total 9059 (delta 42), reused 50 (delta 23), pack-reused 8965
Receiving objects: 100% (9059/9059), 1.80 MiB | 2.44 MiB/s, done.
Resolving deltas: 100% (6114/6114), done.
Tapped 298 formulae (335 files, 2.5MB).
==> Installing mosdepth from brewsci/bio
mosdepth: Linux is required.
Error: An unsatisfied requirement failed this build.
I remember trying to build it from source in the past multiple times on Mac and it never worked (cannot recall exact error messages). I remember I always installed Nim itself manually, maybe using choosenim here took care of any dependencies that were necessary, but this is just guessing.
hi, I have a build here: https://github.com/brentp/mosdepth/actions/runs/101966135
you can download the artifact (it's a zip file) then extract and chmod +x the mosdepth_macos-10.15` binary. if i hear that this is generally working, i'll incorporate these binaries into the next release.
note that these are not static and so still require htslib (brew install htslib).
